Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 46 | Valentino Rossi | Fiat Yamaha Team | 43'09.599 | 24 | 25 | 4 |
| 2 | 1 | Casey Stoner | Ducati Marlboro Team | 43'11.542 | 24 | 20 | 2 |
| 3 | 2 | Dani Pedrosa | Repsol Honda Team | 43'14.465 | 24 | 16 | 5 |
| 4 | 48 | Jorge Lorenzo | Fiat Yamaha Team | 43'15.764 | 24 | 13 | 1 |
| 5 | 69 | Nicky Hayden | Repsol Honda Team | 43'34.192 | 24 | 11 | 3 |
| 6 | 65 | Loris Capirossi | Rizla Suzuki MotoGP | 43'35.284 | 24 | 10 | 6 |
| 7 | 5 | Colin Edwards | Tech3 Yamaha | 43'35.517 | 24 | 9 | 7 |
| 8 | 56 | Shinya Nakano | San Carlo Honda Gresini | 43'35.602 | 24 | 8 | 9 |
| 9 | 4 | Andrea Dovizioso | Jir Team Scot MotoGP | 43'35.818 | 24 | 7 | 13 |
| 10 | 21 | John Hopkins | Kawasaki Racing Team | 43'46.730 | 24 | 6 | 11 |
| 11 | 52 | James Toseland | Tech3 Yamaha | 43'47.173 | 24 | 5 | 10 |
| 12 | 14 | Randy De Puniet | LCR Honda MotoGP | 43'47.619 | 24 | 4 | 8 |
| 13 | 33 | Marco Melandri | Ducati Marlboro Team | 43'49.367 | 24 | 3 | 16 |
| 14 | 50 | Sylvain Guintoli | Alice Team | 43'55.445 | 24 | 2 | 15 |
| 15 | 13 | Anthony West | Kawasaki Racing Team | 44'05.347 | 24 | 1 | 17 |
| 16 | 24 | Toni Elias | Alice Team | 44'08.919 | 24 | 0 | 14 |
| 17 | 15 | Alex De Angelis | San Carlo Honda Gresini | 44'21.997 | 24 | 0 | 18 |
| 18 | 7 | Chris Vermeulen | Rizla Suzuki MotoGP | 29'15.247 | 8 | 0 | 12 |
| 19 | 64 | Kousuke Akiyoshi | Rizla Suzuki MotoGP | 24 | 0 | 19 |