Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 26 | Dani Pedrosa | Repsol Honda Team | 18:11:21 | 24 | 25 | 4 |
| 2 | 1 | Jorge Lorenzo | Yamaha Factory Racing | 20:13:00 | 24 | 20 | 2 |
| 3 | 27 | Casey Stoner | Repsol Honda Team | 23:17:41 | 24 | 16 | 1 |
| 4 | 58 | Marco Simoncelli | San Carlo Honda Gresini | 00:43:51 | 24 | 13 | 6 |
| 5 | 4 | Andrea Dovizioso | Repsol Honda Team | 00:46:12 | 24 | 11 | 3 |
| 6 | 11 | Ben Spies | Yamaha Factory Racing | 04:38:05 | 24 | 10 | 5 |
| 7 | 69 | Nicky Hayden | Ducati Team | 05:04:08 | 24 | 9 | 10 |
| 8 | 5 | Colin Edwards | Monster Yamaha Tech 3 | 06:41:44 | 24 | 8 | 14 |
| 9 | 7 | Hiroshi Aoyama | San Carlo Honda Gresini | 07:49:15 | 24 | 7 | 11 |
| 10 | 14 | Randy De Puniet | Pramac Racing Team | 10:35:03 | 24 | 6 | 13 |
| 11 | 35 | Cal Crutchlow | Monster Yamaha Tech 3 | 14:44:05 | 24 | 5 | 12 |
| 12 | 64 | Kousuke Akiyoshi | San Carlo Honda Gresini | 16:53:10 | 24 | 4 | 17 |
| 13 | 72 | Shinichi Ito | Honda Racing Corporation | 18:11:02 | 24 | 3 | 19 |
| 14 | 46 | Valentino Rossi | Ducati Team | 11:02:45 | 17 | 0 | 7 |
| 15 | 24 | Toni Elias | LCR Honda MotoGP | 11:02:45 | 17 | 0 | 16 |
| 16 | 6 | Damian Cudlin | Pramac Racing Team | 15:18:21 | 13 | 0 | 18 |
| 17 | 19 | Alvaro Bautista | Rizla Suzuki MotoGP | 07:45:28 | 13 | 0 | 8 |
| 18 | 8 | Hector Barbera | Mapfre Aspar Team MotoGP | 09:32:00 | 1 | 0 | 9 |