| 2006-04-03 | vs SFN | 1 | W 6-1 | 1-0 | 2 | 43,767 | Jake Peavy | Jason Schmidt | Jake Peavy | Jason Schmidt | | 6 | 1 | 5 |
| 2006-04-05 | vs SFN | 2 | L 1-3 | 1-1 | 3 | 23,721 | Shawn Estes | Matt Morris | Matt Morris | Shawn Estes | Tim Worrell | 7 | 4 | 3 |
| 2006-04-07 | vs COL | 3 | L 4-10 | 1-2 | 5 | 33,918 | Chris Young | Josh Fogg | Josh Fogg | Clay Hensley | | 11 | 14 | -3 |
| 2006-04-08 | vs COL | 4 | L 4-12 | 1-3 | 5 | 29,629 | Dewon Brazelton | Zach Day | Zach Day | Dewon Brazelton | | 15 | 26 | -11 |
| 2006-04-09 | vs COL | 5 | L 4-10 | 1-4 | 5 | 28,901 | Jake Peavy | Jason Jennings | Jason Jennings | Jake Peavy | | 19 | 36 | -17 |
| 2006-04-11 | @ FLO | 6 | W 9-3 | 2-4 | 5 | 31,308 | Woody Williams | Sergio Mitre | Woody Williams | Sergio Mitre | | 28 | 39 | -11 |
| 2006-04-12 | @ FLO | 7 | W 7-2 | 3-4 | 5 | 8,994 | Chris Young | Brian Moehler | Chris Young | Brian Moehler | | 35 | 41 | -6 |
| 2006-04-13 | @ FLO | 8 | L 2-9 | 3-5 | 5 | 8,191 | Dewon Brazelton | Jason Vargas | Jason Vargas | Dewon Brazelton | | 37 | 50 | -13 |
| 2006-04-14 | @ ATL | 9 | L 4-5 | 3-6 | 5 | 36,406 | Chan Ho Park | Tim Hudson | Oscar Villarreal | Scott Linebrink | Chris Reitsma | 41 | 55 | -14 |
| 2006-04-15 | @ ATL | 10 | L 0-2 | 3-7 | 5 | 40,151 | Jake Peavy | John Smoltz | John Smoltz | Jake Peavy | | 41 | 57 | -16 |
| 2006-04-16 | @ ATL | 11 | W 4-3 | 4-7 | 5 | 24,589 | Woody Williams | John Thomson | Scott Linebrink | Mike Remlinger | Trevor Hoffman | 45 | 60 | -15 |
| 2006-04-17 | @ COL | 12 | W 5-2 | 5-7 | 4 | 18,591 | Chris Young | Jeff Francis | Chris Young | Jeff Francis | Trevor Hoffman | 50 | 62 | -12 |
| 2006-04-18 | @ COL | 13 | L 2-3 | 5-8 | 5 | 18,595 | Clay Hensley | Josh Fogg | David Cortes | Jon Adkins | | 52 | 65 | -13 |
| 2006-04-19 | @ COL | 14 | W 13-4 | 6-8 | 5 | 18,827 | Chan Ho Park | Zach Day | Chan Ho Park | Zach Day | | 65 | 69 | -4 |
| 2006-04-20 | vs NYN | 15 | L 2-7 | 6-9 | 5 | 28,791 | Jake Peavy | Steve Trachsel | Duaner Sanchez | Scott Linebrink | | 67 | 76 | -9 |
| 2006-04-21 | vs NYN | 16 | W 2-1 | 7-9 | 4 | 38,541 | Woody Williams | Brian Bannister | Brian Sweeney | Chad Bradford | | 69 | 77 | -8 |
| 2006-04-22 | vs NYN | 17 | L 1-8 | 7-10 | 5 | 39,389 | Chris Young | Pedro Martinez | Pedro Martinez | Chris Young | | 70 | 85 | -15 |
| 2006-04-23 | vs NYN | 18 | W 7-4 | 8-10 | 4 | 34,109 | Clay Hensley | Victor Zambrano | Clay Hensley | Victor Zambrano | Trevor Hoffman | 77 | 89 | -12 |
| 2006-04-24 | vs ARI | 19 | L 1-4 | 8-11 | 5 | 19,718 | Chan Ho Park | Brandon Webb | Brandon Webb | Chan Ho Park | Jose Valverde | 78 | 93 | -15 |
| 2006-04-25 | vs ARI | 20 | L 0-7 | 8-12 | 5 | 21,281 | Jake Peavy | Claudio Vargas | Claudio Vargas | Jake Peavy | | 78 | 100 | -22 |
| 2006-04-26 | vs ARI | 21 | L 2-3 | 8-13 | 5 | 22,247 | Woody Williams | Orlando Hernandez | Orlando Hernandez | Woody Williams | Jose Valverde | 80 | 103 | -23 |
| 2006-04-28 | vs LAN | 22 | L 0-3 | 8-14 | 5 | 36,435 | Chris Young | Jae Weong Seo | Jae Weong Seo | Chris Young | Danys Baez | 80 | 106 | -26 |
| 2006-04-29 | vs LAN | 23 | L 2-4 | 8-15 | 5 | 44,337 | Clay Hensley | Brett Tomko | Brett Tomko | Clay Hensley | Danys Baez | 82 | 110 | -28 |
| 2006-04-30 | vs LAN | 24 | W 6-5 | 9-15 | 5 | 38,116 | Chan Ho Park | Derek Lowe | Scott Linebrink | Tim Hamulack | | 88 | 115 | -27 |
| 2006-05-01 | @ SFN | 25 | W 10-4 | 10-15 | 5 | 33,780 | Jake Peavy | Jamey Wright | Jake Peavy | Jamey Wright | | 98 | 119 | -21 |
| 2006-05-02 | @ SFN | 26 | W 5-3 | 11-15 | 5 | 34,641 | Woody Williams | Matt Morris | Woody Williams | Matt Morris | Trevor Hoffman | 103 | 122 | -19 |
| 2006-05-03 | @ LAN | 27 | W 11-5 | 12-15 | 4 | 33,352 | Chris Young | Jae Weong Seo | Scott Cassidy | Franquelis Osoria | | 114 | 127 | -13 |
| 2006-05-04 | @ LAN | 28 | W 3-0 | 13-15 | 4 | 34,137 | Clay Hensley | Brett Tomko | Alan Embree | Takashi Saito | Trevor Hoffman | 117 | 127 | -10 |
| 2006-05-05 | vs CHN | 29 | W 1-0 | 14-15 | 3 | 37,123 | Chan Ho Park | Carlos Zambrano | Scott Cassidy | Scott Williamson | | 118 | 127 | -9 |
| 2006-05-06 | vs CHN | 30 | W 2-1 | 15-15 | 3 | 37,745 | Jake Peavy | Sean Marshall | Scott Cassidy | Bob Howry | | 120 | 128 | -8 |
| 2006-05-07 | vs CHN | 31 | W 6-3 | 16-15 | 3 | 39,847 | Woody Williams | Angel Guzman | Woody Williams | Angel Guzman | Brian Sweeney | 126 | 131 | -5 |
| 2006-05-08 | vs CHN | 32 | W 8-3 | 17-15 | 3 | 24,139 | Chris Young | Greg Maddux | Chris Young | Greg Maddux | | 134 | 134 | 0 |
| 2006-05-09 | vs MIL | 33 | L 4-5 | 17-16 | 3 | 22,196 | Clay Hensley | Doug Davis | Danny Kolb | Trevor Hoffman | Derrick Turnbow | 138 | 139 | -1 |
| 2006-05-10 | vs MIL | 34 | W 3-0 | 18-16 | 3 | 20,088 | Chan Ho Park | Chris Capuano | Chan Ho Park | Chris Capuano | Trevor Hoffman | 141 | 139 | 2 |
| 2006-05-11 | vs MIL | 35 | W 8-5 | 19-16 | 3 | 22,500 | Jake Peavy | Ben Hendrickson | Jake Peavy | Ben Hendrickson | | 149 | 144 | 5 |
| 2006-05-12 | @ CHN | 36 | W 10-5 | 20-16 | 2 | 39,245 | Woody Williams | Angel Guzman | Brian Sweeney | Glendon Rusch | | 159 | 149 | 10 |
| 2006-05-13 | @ CHN | 37 | W 4-3 | 21-16 | 2 | 40,095 | Chris Young | Greg Maddux | Cla Meredith | Ryan Dempster | Trevor Hoffman | 163 | 152 | 11 |
| 2006-05-14 | @ CHN | 38 | W 9-0 | 22-16 | 1 | 39,570 | Clay Hensley | Rich Hill | Clay Hensley | Rich Hill | | 172 | 152 | 20 |
| 2006-05-15 | @ ARI | 39 | L 5-6 | 22-17 | 1 | 19,838 | Chan Ho Park | Brandon Webb | Jose Valverde | Scott Cassidy | | 177 | 158 | 19 |
| 2006-05-16 | @ ARI | 40 | L 2-5 | 22-18 | 3 | 20,015 | Jake Peavy | Orlando Hernandez | Jason Grimsley | Jake Peavy | Jose Valverde | 179 | 163 | 16 |
| 2006-05-17 | @ ARI | 41 | W 14-10 | 23-18 | 1 | 18,012 | Mike Thompson | Juan Cruz | Mike Thompson | Juan Cruz | | 193 | 173 | 20 |
| 2006-05-19 | @ SEA | 42 | L 4-7 | 23-19 | 3 | 35,338 | Chris Young | Jarrod Washburn | Rafael Soriano | Scott Cassidy | | 197 | 180 | 17 |
| 2006-05-20 | @ SEA | 43 | L 3-6 | 23-20 | 4 | 33,946 | Clay Hensley | Gil Meche | Gil Meche | Clay Hensley | J.J. Putz | 200 | 186 | 14 |
| 2006-05-21 | @ SEA | 44 | L 8-10 | 23-21 | 4 | 37,132 | Chan Ho Park | Felix Hernandez | Felix Hernandez | Chan Ho Park | J.J. Putz | 208 | 196 | 12 |
| 2006-05-22 | vs ATL | 45 | L 1-3 | 23-22 | 5 | 25,869 | Jake Peavy | John Smoltz | John Smoltz | Jake Peavy | Chris Reitsma | 209 | 199 | 10 |
| 2006-05-23 | vs ATL | 46 | W 2-1 | 24-22 | 4 | 25,315 | Mike Thompson | Jorge Sosa | Mike Thompson | Jorge Sosa | Trevor Hoffman | 211 | 200 | 11 |
| 2006-05-24 | vs ATL | 47 | L 6-10 | 24-23 | 4 | 23,740 | Chris Young | John Thomson | John Thomson | Chris Young | | 217 | 210 | 7 |
| 2006-05-26 | vs SLN | 48 | W 7-1 | 25-23 | 4 | 40,075 | Clay Hensley | Jeff Suppan | Clay Hensley | Jeff Suppan | | 224 | 211 | 13 |
| 2006-05-27 | vs SLN | 49 | L 3-4 | 25-24 | 5 | 32,722 | Chan Ho Park | Sidney Ponson | Sidney Ponson | Chan Ho Park | Jason Isringhausen | 227 | 215 | 12 |
| 2006-05-28 | vs SLN | 50 | W 10-8 | 26-24 | 4 | 38,145 | Jake Peavy | Mark Mulder | Jake Peavy | Mark Mulder | Trevor Hoffman | 237 | 223 | 14 |
| 2006-05-29 | vs COL | 51 | L 0-5 | 26-25 | 4 | 27,904 | Mike Thompson | Jason Jennings | Jason Jennings | Mike Thompson | | 237 | 228 | 9 |
| 2006-05-30 | vs COL | 52 | W 2-0 | 27-25 | 4 | 23,698 | Chris Young | Aaron Cook | Chris Young | Aaron Cook | Trevor Hoffman | 239 | 228 | 11 |
| 2006-05-31 | vs COL | 53 | W 3-2 | 28-25 | 3 | 24,607 | Clay Hensley | Jeff Francis | Clay Hensley | Jeff Francis | Trevor Hoffman | 242 | 230 | 12 |
| 2006-06-02 | @ PIT | 54 | W 7-0 | 29-25 | 3 | 20,777 | Chan Ho Park | Oliver Perez | Chan Ho Park | Oliver Perez | | 249 | 230 | 19 |
| 2006-06-03 | @ PIT | 55 | L 4-6 | 29-26 | 3 | 30,639 | Mike Thompson | Zach Duke | Zach Duke | Mike Thompson | Mike Gonzalez | 253 | 236 | 17 |
| 2006-06-04 | @ PIT | 56 | W 1-0 | 30-26 | 3 | 26,857 | Chris Young | Victor Santos | Chris Young | Victor Santos | Trevor Hoffman | 254 | 236 | 18 |
| 2006-06-05 | @ MIL | 57 | L 2-5 | 30-27 | 3 | 13,611 | Clay Hensley | Chris Capuano | Chris Capuano | Clay Hensley | Derrick Turnbow | 256 | 241 | 15 |
| 2006-06-06 | @ MIL | 58 | L 1-5 | 30-28 | 4 | 14,722 | Jake Peavy | David Bush | David Bush | Jake Peavy | | 257 | 246 | 11 |
| 2006-06-07 | @ MIL | 59 | W 6-5 | 31-28 | 3 | 16,982 | Chan Ho Park | Zach Jackson | Scott Cassidy | Matt Wise | Trevor Hoffman | 263 | 251 | 12 |
| 2006-06-08 | @ MIL | 60 | L 3-4 | 31-29 | 4 | 20,510 | Mike Thompson | Doug Davis | Derrick Turnbow | Scott Cassidy | | 266 | 255 | 11 |
| 2006-06-09 | vs FLO | 61 | W 3-2 | 32-29 | 3 | 32,247 | Chris Young | Ricky Nolasco | Chris Young | Ricky Nolasco | Trevor Hoffman | 269 | 257 | 12 |
| 2006-06-10 | vs FLO | 62 | L 1-2 | 32-30 | 3 | 31,567 | Clay Hensley | Scott Olsen | Scott Olsen | Clay Hensley | Joe Borowski | 270 | 259 | 11 |
| 2006-06-11 | vs FLO | 63 | L 3-7 | 32-31 | 3 | 31,090 | Jake Peavy | Brian Moehler | Brian Moehler | Jake Peavy | Taylor Tankersley | 273 | 266 | 7 |
| 2006-06-13 | vs LAN | 64 | W 9-1 | 33-31 | 3 | 30,371 | Chan Ho Park | Aaron Sele | Chan Ho Park | Aaron Sele | | 282 | 267 | 15 |
| 2006-06-14 | vs LAN | 65 | W 5-3 | 34-31 | 3 | 30,011 | Mike Thompson | Brad Penny | Scott Linebrink | Hong-Chih Kuo | Trevor Hoffman | 287 | 270 | 17 |
| 2006-06-15 | vs LAN | 66 | L 3-7 | 34-32 | 4 | 33,382 | Chris Young | Chad Billingsley | Jonathan Broxton | Brian Sikorski | | 290 | 277 | 13 |
| 2006-06-16 | @ ANA | 67 | W 5-4 | 35-32 | 3 | 44,005 | Clay Hensley | Jeff Weaver | Alan Embree | Francisco Rodriguez | Trevor Hoffman | 295 | 281 | 14 |
| 2006-06-17 | @ ANA | 68 | L 2-3 | 35-33 | 3 | 43,909 | Jake Peavy | Ervin Santana | Ervin Santana | Jake Peavy | Francisco Rodriguez | 297 | 284 | 13 |
| 2006-06-18 | @ ANA | 69 | W 7-3 | 36-33 | 2 | 44,159 | Chan Ho Park | Bartolo Colon | Chan Ho Park | Bartolo Colon | | 304 | 287 | 17 |
| 2006-06-20 | @ TEX | 70 | W 6-5 | 37-33 | 1 | 24,064 | Mike Thompson | Vicente Padilla | Mike Thompson | Scott Feldman | Trevor Hoffman | 310 | 292 | 18 |
| 2006-06-21 | @ TEX | 71 | W 3-2 | 38-33 | 1 | 29,047 | Chris Young | Kevin Millwood | Scott Linebrink | Akinori Otsuka | Trevor Hoffman | 313 | 294 | 19 |
| 2006-06-22 | @ TEX | 72 | L 3-5 | 38-34 | 1 | 24,637 | Clay Hensley | John Rheinecker | John Rheinecker | Clay Hensley | Akinori Otsuka | 316 | 299 | 17 |
| 2006-06-23 | vs SEA | 73 | W 2-1 | 39-34 | 1 | 40,049 | Jake Peavy | Gil Meche | Scott Linebrink | Julio Mateo | | 318 | 300 | 18 |
| 2006-06-24 | vs SEA | 74 | L 5-9 | 39-35 | 2 | 33,349 | Chan Ho Park | Jamie Moyer | Jamie Moyer | Chan Ho Park | | 323 | 309 | 14 |
| 2006-06-25 | vs SEA | 75 | L 4-9 | 39-36 | 2 | 32,707 | Mike Thompson | Joel Pineiro | George Sherrill | Alan Embree | | 327 | 318 | 9 |
| 2006-06-27 | vs OAK | 76 | W 3-0 | 40-36 | 1 | 34,102 | Chris Young | Barry Zito | Chris Young | Barry Zito | Trevor Hoffman | 330 | 318 | 12 |
| 2006-06-28 | vs OAK | 77 | W 8-1 | 41-36 | 1 | 39,874 | Clay Hensley | Joe Blanton | Clay Hensley | Joe Blanton | | 338 | 319 | 19 |
| 2006-06-29 | vs OAK | 78 | L 5-6 | 41-37 | 1 | 30,301 | Jake Peavy | Dan Haren | Ron Flores | Scott Cassidy | Chad Gaudin | 343 | 325 | 18 |
| 2006-06-30 | vs SFN | 79 | W 6-5 | 42-37 | 1 | 39,511 | Chan Ho Park | Jamey Wright | Brian Sikorski | Jeremy Accardo | | 349 | 330 | 19 |
| 2006-07-01 | vs SFN | 80 | W 7-4 | 43-38 | 1 | 23,888 | Mike Thompson | Matt Cain | Jon Adkins | Brian Wilson | Trevor Hoffman | 356 | 334 | 22 |
| 2006-07-01 | vs SFN | 81 | L 1-4 | 43-38 | 1 | 43,029 | Woody Williams | Brad Hennessey | Steve Kline | Alan Embree | Armando Benitez | 357 | 338 | 19 |
| 2006-07-02 | vs SFN | 82 | L 2-6 | 43-39 | 1 | 39,837 | Chris Young | Matt Morris | Matt Morris | Chris Young | Brian Wilson | 359 | 344 | 15 |
| 2006-07-04 | @ PHI | 83 | L 5-6 | 43-40 | 3 | 29,192 | Clay Hensley | Cole Hamels | Tom Gordon | Cla Meredith | | 364 | 350 | 14 |
| 2006-07-05 | @ PHI | 84 | W 6-3 | 44-40 | 3 | 40,230 | Jake Peavy | Scott Mathieson | Scott Linebrink | Arthur Rhodes | Trevor Hoffman | 370 | 353 | 17 |
| 2006-07-06 | @ PHI | 85 | W 5-3 | 45-40 | 1 | 30,261 | Chan Ho Park | Ryan Madson | Chan Ho Park | Ryan Madson | Trevor Hoffman | 375 | 356 | 19 |
| 2006-07-07 | @ WAS | 86 | W 3-2 | 46-40 | 1 | 25,161 | Woody Williams | Ramon Ortiz | Woody Williams | Ramon Ortiz | Trevor Hoffman | 378 | 358 | 20 |
| 2006-07-08 | @ WAS | 87 | W 5-2 | 47-40 | 1 | 27,060 | Chris Young | Pedro Astacio | Chris Young | Pedro Astacio | Trevor Hoffman | 383 | 360 | 23 |
| 2006-07-09 | @ WAS | 88 | W 10-9 | 48-40 | 1 | 22,000 | Clay Hensley | John Patterson | Scott Cassidy | Chad Cordero | Scott Linebrink | 393 | 369 | 24 |
| 2006-07-14 | vs ATL | 89 | L 12-15 | 48-41 | 1 | 42,869 | Chris Young | Tim Hudson | Jorge Sosa | Clay Hensley | Tyler Yates | 405 | 384 | 21 |
| 2006-07-15 | vs ATL | 90 | L 3-11 | 48-42 | 1 | 39,988 | Chan Ho Park | John Smoltz | John Smoltz | Chan Ho Park | | 408 | 395 | 13 |
| 2006-07-16 | vs ATL | 91 | L 5-10 | 48-43 | 1 | 31,650 | Jake Peavy | Chuck James | Chuck James | Jake Peavy | | 413 | 405 | 8 |
| 2006-07-17 | vs PHI | 92 | W 8-6 | 49-43 | 1 | 25,936 | Woody Williams | Cole Hamels | Alan Embree | Rheal Cormier | Trevor Hoffman | 421 | 411 | 10 |
| 2006-07-18 | vs PHI | 93 | W 10-6 | 50-43 | 1 | 33,327 | Clay Hensley | Ryan Madson | Clay Hensley | Ryan Madson | | 431 | 417 | 14 |
| 2006-07-19 | vs PHI | 94 | L 4-5 | 50-44 | 1 | 32,101 | Mike Thompson | Jon Lieber | Geoff Geary | Trevor Hoffman | Tom Gordon | 435 | 422 | 13 |
| 2006-07-20 | @ SFN | 95 | L 3-9 | 50-45 | 1 | 42,047 | Chan Ho Park | Noah Lowry | Noah Lowry | Chan Ho Park | | 438 | 431 | 7 |
| 2006-07-21 | @ SFN | 96 | L 2-8 | 50-46 | 1 | 42,683 | Jake Peavy | Matt Cain | Matt Cain | Jake Peavy | | 440 | 439 | 1 |
| 2006-07-22 | @ SFN | 97 | L 3-4 | 50-47 | 3 | 42,955 | Woody Williams | Jason Schmidt | Jason Schmidt | Woody Williams | Armando Benitez | 443 | 443 | 0 |
| 2006-07-23 | @ SFN | 98 | W 6-5 | 51-47 | 1 | 41,209 | Clay Hensley | Jamey Wright | Jon Adkins | Brian Wilson | Trevor Hoffman | 449 | 448 | 1 |
| 2006-07-24 | @ LAN | 99 | W 7-6 | 52-47 | 1 | 38,050 | Chris Young | Derek Lowe | Doug Brocail | Giovanni Carrara | Trevor Hoffman | 456 | 454 | 2 |
| 2006-07-25 | @ LAN | 100 | W 7-3 | 53-47 | 1 | 51,334 | Chan Ho Park | Mark Hendrickson | Chan Ho Park | Mark Hendrickson | | 463 | 457 | 6 |
| 2006-07-26 | @ LAN | 101 | W 10-3 | 54-47 | 1 | 44,181 | Jake Peavy | Brad Penny | Jake Peavy | Brad Penny | | 473 | 460 | 13 |
| 2006-07-27 | @ COL | 102 | L 8-9 | 54-48 | 1 | 24,260 | Woody Williams | Josh Fogg | Brian Fuentes | Scott Williamson | | 481 | 469 | 12 |
| 2006-07-28 | @ COL | 103 | L 1-3 | 54-49 | 1 | 28,790 | Clay Hensley | Byung-Hyun Kim | Byung-Hyun Kim | Clay Hensley | Brian Fuentes | 482 | 472 | 10 |
| 2006-07-29 | @ COL | 104 | W 4-2 | 55-49 | 1 | 43,433 | Chris Young | Jeff Francis | Chris Young | Jeff Francis | Trevor Hoffman | 486 | 474 | 12 |
| 2006-07-30 | @ COL | 105 | L 1-3 | 55-50 | 1 | 25,790 | Mike Thompson | Jason Jennings | Jason Jennings | Mike Thompson | Brian Fuentes | 487 | 477 | 10 |
| 2006-08-01 | vs HOU | 106 | L 0-1 | 55-51 | 1 | 39,925 | Jake Peavy | Andy Pettitte | Andy Pettitte | Jake Peavy | Brad Lidge | 487 | 478 | 9 |
| 2006-08-02 | vs HOU | 107 | L 1-7 | 55-52 | 1 | 30,757 | Woody Williams | Brandon Backe | Brandon Backe | Woody Williams | | 488 | 485 | 3 |
| 2006-08-03 | vs HOU | 108 | W 5-2 | 56-52 | 1 | 29,661 | Clay Hensley | Matt Albers | Clay Hensley | Matt Albers | Trevor Hoffman | 493 | 487 | 6 |
| 2006-08-04 | vs WAS | 109 | L 2-6 | 56-53 | 1 | 36,538 | Chris Young | Ramon Ortiz | Ramon Ortiz | Chris Young | | 495 | 493 | 2 |
| 2006-08-05 | vs WAS | 110 | W 6-3 | 57-53 | 1 | 40,339 | Mike Thompson | Pedro Astacio | Alan Embree | Pedro Astacio | Trevor Hoffman | 501 | 496 | 5 |
| 2006-08-06 | vs WAS | 111 | W 3-2 | 58-53 | 1 | 35,648 | Jake Peavy | Livan Hernandez | Doug Brocail | Micah Bowie | | 504 | 498 | 6 |
| 2006-08-08 | @ NYN | 112 | L 2-3 | 58-54 | 1 | 46,167 | Woody Williams | Steve Trachsel | Steve Trachsel | Woody Williams | Billy Wagner | 506 | 501 | 5 |
| 2006-08-09 | @ NYN | 113 | L 3-4 | 58-55 | 1 | 49,979 | Clay Hensley | Pedro Martinez | Pedro Martinez | Clay Hensley | Billy Wagner | 509 | 505 | 4 |
| 2006-08-10 | @ NYN | 114 | L 3-7 | 58-56 | 3 | 39,649 | Chris Young | Orlando Hernandez | Orlando Hernandez | Doug Brocail | | 512 | 512 | 0 |
| 2006-08-11 | @ HOU | 115 | L 2-4 | 58-57 | 3 | 43,239 | Chan Ho Park | Andy Pettitte | Andy Pettitte | Chan Ho Park | Brad Lidge | 514 | 516 | -2 |
| 2006-08-12 | @ HOU | 116 | W 6-3 | 59-57 | 3 | 43,591 | Jake Peavy | Jason Hirsh | Jake Peavy | Jason Hirsh | Trevor Hoffman | 520 | 519 | 1 |
| 2006-08-13 | @ HOU | 117 | W 7-2 | 60-57 | 2 | 43,143 | Woody Williams | Brandon Backe | Woody Williams | Brandon Backe | | 527 | 521 | 6 |
| 2006-08-14 | vs SFN | 118 | L 0-1 | 60-58 | 2 | 31,774 | Clay Hensley | Brad Hennessey | Brad Hennessey | Clay Hensley | Armando Benitez | 527 | 522 | 5 |
| 2006-08-15 | vs SFN | 119 | L 2-3 | 60-59 | 3 | 31,601 | Chris Young | Matt Morris | Mike Stanton | Scott Linebrink | Armando Benitez | 529 | 525 | 4 |
| 2006-08-16 | vs SFN | 120 | L 5-7 | 60-60 | 3 | 33,938 | Chan Ho Park | Noah Lowry | Steve Kline | Alan Embree | Mike Stanton | 534 | 532 | 2 |
| 2006-08-17 | vs SFN | 121 | L 4-8 | 60-61 | 3 | 29,734 | Jake Peavy | Matt Cain | Matt Cain | Jake Peavy | | 538 | 540 | -2 |
| 2006-08-18 | vs ARI | 122 | W 8-2 | 61-61 | 3 | 35,196 | Woody Williams | Enrique Gonzalez | Woody Williams | Enrique Gonzalez | | 546 | 542 | 4 |
| 2006-08-19 | vs ARI | 123 | L 3-5 | 61-62 | 3 | 34,250 | Mike Thompson | Claudio Vargas | Claudio Vargas | Mike Thompson | Tony Pena | 549 | 547 | 2 |
| 2006-08-20 | vs ARI | 124 | W 2-1 | 62-62 | 3 | 34,843 | Chris Young | Miguel Batista | Cla Meredith | Brandon Medders | | 551 | 548 | 3 |
| 2006-08-21 | vs LAN | 125 | W 4-2 | 63-62 | 2 | 33,244 | Tim Stauffer | Chad Billingsley | Tim Stauffer | Elmer Dessens | Trevor Hoffman | 555 | 550 | 5 |
| 2006-08-22 | vs LAN | 126 | W 1-0 | 64-62 | 2 | 32,774 | Jake Peavy | Mark Hendrickson | Jake Peavy | Mark Hendrickson | Trevor Hoffman | 556 | 550 | 6 |
| 2006-08-23 | vs LAN | 127 | W 7-2 | 65-62 | 2 | 36,613 | Woody Williams | Brad Penny | Woody Williams | Brad Penny | | 563 | 552 | 11 |
| 2006-08-25 | @ COL | 128 | L 5-13 | 65-63 | 2 | 24,182 | Mike Thompson | Jeff Francis | Jeff Francis | Mike Thompson | | 568 | 565 | 3 |
| 2006-08-26 | @ COL | 129 | W 5-2 | 66-63 | 2 | 29,748 | Clay Hensley | Jason Jennings | Clay Hensley | Jason Jennings | Trevor Hoffman | 573 | 567 | 6 |
| 2006-08-27 | @ COL | 130 | L 3-6 | 66-64 | 2 | 26,308 | Jake Peavy | Aaron Cook | Aaron Cook | Jake Peavy | | 576 | 573 | 3 |
| 2006-08-28 | @ ARI | 131 | L 4-7 | 66-65 | 2 | 29,269 | Woody Williams | Brandon Webb | Brandon Webb | Woody Williams | | 580 | 580 | 0 |
| 2006-08-29 | @ ARI | 132 | W 8-3 | 67-65 | 2 | 21,551 | Chris Young | Enrique Gonzalez | Chris Young | Enrique Gonzalez | | 588 | 583 | 5 |
| 2006-08-30 | @ ARI | 133 | W 4-1 | 68-65 | 2 | 20,223 | Mike Thompson | Claudio Vargas | Mike Thompson | Claudio Vargas | Trevor Hoffman | 592 | 584 | 8 |
| 2006-09-01 | vs CIN | 134 | L 2-6 | 68-66 | 2 | 32,901 | Clay Hensley | Bronson Arroyo | Bronson Arroyo | Clay Hensley | | 594 | 590 | 4 |
| 2006-09-02 | vs CIN | 135 | W 7-1 | 69-66 | 2 | 36,287 | Jake Peavy | Kyle Lohse | Jake Peavy | Kyle Lohse | | 601 | 591 | 10 |
| 2006-09-03 | vs CIN | 136 | W 2-1 | 70-66 | 2 | 31,153 | David Wells | Eric Milton | Cla Meredith | Rheal Cormier | Trevor Hoffman | 603 | 592 | 11 |
| 2006-09-04 | vs COL | 137 | W 7-5 | 71-66 | 2 | 35,722 | Woody Williams | Josh Fogg | Rudy Seanez | Brian Fuentes | | 610 | 597 | 13 |
| 2006-09-05 | vs COL | 138 | W 5-4 | 72-66 | 2 | 26,456 | Chris Young | Jeff Francis | Cla Meredith | Jeff Francis | Trevor Hoffman | 615 | 601 | 14 |
| 2006-09-06 | vs COL | 139 | W 2-0 | 73-66 | 2 | 27,968 | Clay Hensley | Jason Jennings | Cla Meredith | Nate Field | | 617 | 601 | 16 |
| 2006-09-08 | @ SFN | 140 | L 0-4 | 73-67 | 2 | 38,988 | Jake Peavy | Matt Cain | Matt Cain | Jake Peavy | | 617 | 605 | 12 |
| 2006-09-09 | @ SFN | 141 | L 4-5 | 73-68 | 2 | 38,680 | David Wells | Jason Schmidt | Mike Stanton | Rudy Seanez | | 621 | 610 | 11 |
| 2006-09-10 | @ SFN | 142 | W 10-2 | 74-68 | 2 | 36,757 | Woody Williams | Matt Morris | Woody Williams | Matt Morris | | 631 | 612 | 19 |
| 2006-09-12 | @ CIN | 143 | L 4-5 | 74-69 | 2 | 15,820 | Chris Young | Eric Milton | Scott Schoeneweis | Doug Brocail | | 635 | 617 | 18 |
| 2006-09-13 | @ CIN | 144 | W 10-0 | 75-69 | 2 | 21,602 | Jake Peavy | Kyle Lohse | Jake Peavy | Kyle Lohse | | 645 | 617 | 28 |
| 2006-09-14 | @ CIN | 145 | W 4-2 | 76-69 | 2 | 16,957 | Clay Hensley | Aaron Harang | Clay Hensley | Aaron Harang | Trevor Hoffman | 649 | 619 | 30 |
| 2006-09-15 | @ LAN | 146 | L 1-3 | 76-70 | 2 | 52,911 | David Wells | Greg Maddux | Greg Maddux | David Wells | Takashi Saito | 650 | 622 | 28 |
| 2006-09-16 | @ LAN | 147 | W 11-2 | 77-70 | 2 | 55,781 | Woody Williams | Chad Billingsley | Woody Williams | Chad Billingsley | Brian Sweeney | 661 | 624 | 37 |
| 2006-09-17 | @ LAN | 148 | W 2-1 | 78-70 | 1 | 54,601 | Chris Young | Derek Lowe | Scott Linebrink | Jonathan Broxton | Trevor Hoffman | 663 | 625 | 38 |
| 2006-09-18 | @ LAN | 149 | L 10-11 | 78-71 | 2 | 55,831 | Jake Peavy | Brad Penny | Aaron Sele | Rudy Seanez | | 673 | 636 | 37 |
| 2006-09-19 | vs ARI | 150 | W 5-2 | 79-71 | 1 | 29,067 | Clay Hensley | Livan Hernandez | Clay Hensley | Livan Hernandez | Trevor Hoffman | 678 | 638 | 40 |
| 2006-09-20 | vs ARI | 151 | L 2-8 | 79-72 | 1 | 34,129 | David Wells | Edgar Gonzalez | Edgar Gonzalez | David Wells | | 680 | 646 | 34 |
| 2006-09-21 | vs ARI | 152 | W 3-1 | 80-72 | 1 | 34,238 | Woody Williams | Brandon Webb | Woody Williams | Brandon Webb | Trevor Hoffman | 683 | 647 | 36 |
| 2006-09-22 | vs PIT | 153 | W 6-2 | 81-72 | 1 | 40,077 | Chris Young | Tom Gorzelanny | Chris Young | Tom Gorzelanny | | 689 | 649 | 40 |
| 2006-09-23 | vs PIT | 154 | W 2-1 | 82-72 | 1 | 43,168 | Jake Peavy | Zach Duke | Jake Peavy | Zach Duke | Trevor Hoffman | 691 | 650 | 41 |
| 2006-09-24 | vs PIT | 155 | W 2-1 | 83-72 | 1 | 41,932 | Clay Hensley | Marty McLeary | Clay Hensley | Juan Perez | Trevor Hoffman | 693 | 651 | 42 |
| 2006-09-25 | @ SLN | 156 | W 6-5 | 84-72 | 1 | 40,149 | Mike Thompson | Jeff Suppan | Scott Cassidy | Brad Thompson | Scott Linebrink | 699 | 656 | 43 |
| 2006-09-26 | @ SLN | 157 | W 7-5 | 85-72 | 1 | 40,443 | Woody Williams | Chris Carpenter | Woody Williams | Chris Carpenter | Trevor Hoffman | 706 | 661 | 45 |
| 2006-09-27 | @ SLN | 158 | L 2-4 | 85-73 | 1 | 40,358 | Chris Young | Anthony Reyes | Tyler Johnson | Scott Linebrink | Adam Wainwright | 708 | 665 | 43 |
| 2006-09-28 | @ ARI | 159 | W 12-4 | 86-73 | 1 | 26,689 | Jake Peavy | Miguel Batista | Jake Peavy | Miguel Batista | | 720 | 669 | 51 |
| 2006-09-29 | @ ARI | 160 | L 1-3 | 86-74 | 2 | 30,700 | Clay Hensley | Livan Hernandez | Livan Hernandez | Clay Hensley | Jose Valverde | 721 | 672 | 49 |
| 2006-09-30 | @ ARI | 161 | W 3-1 | 87-74 | 2 | 33,019 | David Wells | Juan Cruz | David Wells | Edgar Gonzalez | Trevor Hoffman | 724 | 673 | 51 |
| 2006-10-01 | @ ARI | 162 | W 7-6 | 88-74 | 2 | 48,946 | Woody Williams | Brandon Webb | Woody Williams | Brandon Webb | Trevor Hoffman | 731 | 679 | 52 |