Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 46 | Valentino Rossi | Fiat Yamaha Team | 00:19:59 | 24 | 25 | 4 |
| 2 | 1 | Casey Stoner | Ducati Marlboro Team | 00:52:22 | 24 | 20 | 2 |
| 3 | 2 | Dani Pedrosa | Repsol Honda Team | 01:41:05 | 24 | 16 | 5 |
| 4 | 48 | Jorge Lorenzo | Fiat Yamaha Team | 02:02:44 | 24 | 13 | 1 |
| 5 | 69 | Nicky Hayden | Repsol Honda Team | 07:09:52 | 24 | 11 | 3 |
| 6 | 65 | Loris Capirossi | Rizla Suzuki MotoGP | 07:28:04 | 24 | 10 | 6 |
| 7 | 5 | Colin Edwards | Tech3 Yamaha | 07:31:57 | 24 | 9 | 7 |
| 8 | 56 | Shinya Nakano | San Carlo Honda Gresini | 07:33:22 | 24 | 8 | 9 |
| 9 | 4 | Andrea Dovizioso | Jir Team Scot MotoGP | 07:36:58 | 24 | 7 | 13 |
| 10 | 21 | John Hopkins | Kawasaki Racing Team | 10:38:50 | 24 | 6 | 11 |
| 11 | 52 | James Toseland | Tech3 Yamaha | 10:46:13 | 24 | 5 | 10 |
| 12 | 14 | Randy De Puniet | LCR Honda MotoGP | 10:53:39 | 24 | 4 | 8 |
| 13 | 33 | Marco Melandri | Ducati Marlboro Team | 11:22:47 | 24 | 3 | 16 |
| 14 | 50 | Sylvain Guintoli | Alice Team | 13:04:05 | 24 | 2 | 15 |
| 15 | 13 | Anthony West | Kawasaki Racing Team | 15:49:07 | 24 | 1 | 17 |
| 16 | 24 | Toni Elias | Alice Team | 16:48:39 | 24 | 0 | 14 |
| 17 | 15 | Alex De Angelis | San Carlo Honda Gresini | 20:26:37 | 24 | 0 | 18 |
| 18 | 7 | Chris Vermeulen | Rizla Suzuki MotoGP | 08:34:07 | 8 | 0 | 12 |
| 19 | 64 | Kousuke Akiyoshi | Rizla Suzuki MotoGP | 01:00:00 | 24 | 0 | 19 |