Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 99 | Jorge Lorenzo | Fiat Yamaha Team | 43'47.238 | 24 | 25 | 3 |
| 2 | 46 | Valentino Rossi | Fiat Yamaha Team | 43'48.542 | 24 | 20 | 1 |
| 3 | 3 | Dani Pedrosa | Repsol Honda Team | 43'51.001 | 24 | 16 | 11 |
| 4 | 27 | Casey Stoner | Ducati Marlboro Team | 43'52.929 | 24 | 13 | 2 |
| 5 | 4 | Andrea Dovizioso | Repsol Honda Team | 43'56.445 | 24 | 11 | 7 |
| 6 | 33 | Marco Melandri | Kawasaki Racing Team | 44'17.793 | 24 | 10 | 8 |
| 7 | 65 | Loris Capirossi | Rizla Suzuki MotoGP | 44'19.994 | 24 | 9 | 6 |
| 8 | 36 | Mika Kallio | Pramac Racing | 44'26.654 | 24 | 8 | 17 |
| 9 | 52 | James Toseland | Tech3 Yamaha | 44'30.344 | 24 | 7 | 10 |
| 10 | 7 | Chris Vermeulen | Rizla Suzuki MotoGP | 44'30.483 | 24 | 6 | 4 |
| 11 | 14 | Randy De Puniet | LCR Honda MotoGP | 44'32.072 | 24 | 5 | 16 |
| 12 | 5 | Colin Edwards | Tech3 Yamaha | 44'33.778 | 24 | 4 | 5 |
| 13 | 15 | Alex De Angelis | San Carlo Honda Gresini | 44'40.763 | 24 | 3 | 15 |
| 14 | 88 | Niccolo Canepa | Pramac Racing | 45'09.042 | 24 | 2 | 18 |
| 15 | 24 | Toni Elias | San Carlo Honda Gresini | 44'25.681 | 23 | 1 | 9 |
| 16 | 59 | Sete Gibernau | Grupo Franciscio Hermando | 41'40.115 | 17 | 0 | 14 |
| 17 | 69 | Nicky Hayden | Ducati Marlboro Team | 0 | 0 | 12 | |
| 18 | 72 | Yuki Takahashi | Scot Racing Team MotoGP | 0 | 0 | 13 |