Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 26 | Dani Pedrosa | Repsol Honda Team | 42'47.481 | 24 | 25 | 4 |
| 2 | 1 | Jorge Lorenzo | Yamaha Factory Racing | 42'54.780 | 24 | 20 | 2 |
| 3 | 27 | Casey Stoner | Repsol Honda Team | 43'05.861 | 24 | 16 | 1 |
| 4 | 58 | Marco Simoncelli | San Carlo Honda Gresini | 43'11.031 | 24 | 13 | 6 |
| 5 | 4 | Andrea Dovizioso | Repsol Honda Team | 43'11.172 | 24 | 11 | 3 |
| 6 | 11 | Ben Spies | Yamaha Factory Racing | 43'25.085 | 24 | 10 | 5 |
| 7 | 69 | Nicky Hayden | Ducati Team | 43'26.648 | 24 | 9 | 10 |
| 8 | 5 | Colin Edwards | Monster Yamaha Tech 3 | 43'32.504 | 24 | 8 | 14 |
| 9 | 7 | Hiroshi Aoyama | San Carlo Honda Gresini | 43'36.555 | 24 | 7 | 11 |
| 10 | 14 | Randy De Puniet | Pramac Racing Team | 43'46.503 | 24 | 6 | 13 |
| 11 | 35 | Cal Crutchlow | Monster Yamaha Tech 3 | 44'01.445 | 24 | 5 | 12 |
| 12 | 64 | Kousuke Akiyoshi | San Carlo Honda Gresini | 44'09.190 | 24 | 4 | 17 |
| 13 | 72 | Shinichi Ito | Honda Racing Corporation | 44'13.862 | 24 | 3 | 19 |
| 14 | 46 | Valentino Rossi | Ducati Team | 30'50.565 | 17 | 0 | 7 |
| 15 | 24 | Toni Elias | LCR Honda MotoGP | 30'50.565 | 17 | 0 | 16 |
| 16 | 6 | Damian Cudlin | Pramac Racing Team | 23'53.901 | 13 | 0 | 18 |
| 17 | 19 | Alvaro Bautista | Rizla Suzuki MotoGP | 23'26.728 | 13 | 0 | 8 |
| 18 | 8 | Hector Barbera | Mapfre Aspar Team MotoGP | 1'57.120 | 1 | 0 | 9 |