| Stage 3: San José to Modesto, 167.7 km |
| 1 Thor Hushovd (Nor) Cervelo Test Team | 4:28:12 |
| 2 Oscar Freire (Esp) Rabobank |
| 3 Mark Renshaw (Aus) Team Columbia - Highroad |
| 4 Tyler Farrar (USA) Garmin - Slipstream |
| 5 Mark Cavendish (GBr) Team Columbia - Highroad |
| 6 Brett Lancaster (Aus) Cervelo Test Team |
| 7 Lucas Sebastian Haedo (Arg) Colavita / Sutter Home p/b Cooking Light |
| 8 Freddy Rodriguez (USA) Rock Racing |
| 9 Markus Zberg (Sui) BMC Racing Team |
| 10 Pedro Horrillo (Esp) Rabobank |
|
| 39 Svein Tuft (Can) Garmin - Slipstream |
| 42 Dominique Rollin (Can) Cervelo Test Team |
| 87 Will Routley (Can) Jelly Belly Cycling Team |
| 92 Michael Barry (Can) Team Columbia - Highroad |
| 103 Cameron Evans (Can) OUCH Presented By Maxxis | all s.t.* |
|
| *Disqualified for hanging onto car |
|
| GC |
| 1 Levi Leipheimer (USA) Astana | 13:51:14 |
| 2 Michael Rogers (Aus) Team Columbia - Highroad | at 0:24 |
| 3 David Zabriskie (USA) Garmin - Slipstream | 0:28 |
| 4 Lance Armstrong (USA) Astana | 0:30 |
| 5 Christopher Horner (USA) Astana | 0:34 |
| 6 Janez Brajkovic (Slo) Astana | 0:38 |
| 7 Thomas Lovkvist (Swe) Team Columbia - Highroad |
| 8 José Luis Rubiera (Esp) Astana |
| 9 Vincenzo Nibali (Ita) Liquigas | all s.t. |
| 10 Robert Gesink (Ned) Rabobank | 0:39 |
|
| 40 Dominique Rollin (Can) Cervelo Test Team | 8:21 |
| 45 Will Routley (Can) Jelly Belly Cycling Team | 9:26 |
| 48 Cameron Evans (Can) OUCH Presented By Maxxis | 14:50* |
| 51 Svein Tuft (Can) Garmin - Slipstream | 15:13 |
| 97 Michael Barry (Can) Team Columbia - Highroad | 30:02 |
