Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 27 | Casey Stoner | Ducati Marlboro Team | 01:04:26 | 24 | 25 | 3 |
| 2 | 4 | Andrea Dovizioso | Repsol Honda Team | 02:08:54 | 24 | 20 | 1 |
| 3 | 46 | Valentino Rossi | Fiat Yamaha Team | 02:39:33 | 24 | 16 | 2 |
| 4 | 99 | Jorge Lorenzo | Fiat Yamaha Team | 02:48:07 | 24 | 13 | 4 |
| 5 | 5 | Colin Edwards | Tech3 Yamaha | 08:35:58 | 24 | 11 | 5 |
| 6 | 58 | Marco Simoncelli | San Carlo Honda Gresini | 09:24:47 | 24 | 10 | 8 |
| 7 | 19 | Alvaro Bautista | Rizla Suzuki MotoGP | 09:54:52 | 24 | 9 | 9 |
| 8 | 11 | Ben Spies | Tech3 Yamaha | 10:57:18 | 24 | 8 | 6 |
| 9 | 14 | Randy De Puniet | LCR Honda MotoGP | 14:17:10 | 24 | 7 | 7 |
| 10 | 7 | Hiroshi Aoyama | Interwetten Honda MotoGP | 14:51:04 | 24 | 6 | 14 |
| 11 | 33 | Marco Melandri | San Carlo Honda Gresini | 14:57:45 | 24 | 5 | 12 |
| 12 | 69 | Nicky Hayden | Ducati Marlboro Team | 15:09:29 | 24 | 4 | 11 |
| 13 | 40 | Hector Barbera | Paginas Amarillas Aspar | 15:21:28 | 24 | 3 | 15 |
| 14 | 41 | Aleix Espargaro | Pramac Racing | 15:45:09 | 24 | 2 | 13 |
| 15 | 36 | Mika Kallio | Pramac Racing | 21:48:54 | 24 | 1 | 16 |
| 16 | 65 | Loris Capirossi | Rizla Suzuki MotoGP | 14:58:12 | 21 | 0 | 10 |