Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 65 | Loris Capirossi | Ducati Marlboro Team | 01:26:25 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Fiat Yamaha Team | 02:51:13 | 24 | 20 | 2 |
| 3 | 33 | Marco Melandri | Fortuna Honda | 03:46:03 | 24 | 16 | 3 |
| 4 | 15 | Sete Gibernau | Ducati Marlboro Team | 04:08:17 | 24 | 13 | 5 |
| 5 | 69 | Nicky Hayden | Repsol Honda Team | 04:45:29 | 24 | 11 | 7 |
| 6 | 24 | Toni Elias | Fortuna Honda | 06:28:13 | 24 | 10 | 6 |
| 7 | 26 | Dani Pedrosa | Repsol Honda Team | 06:58:42 | 24 | 9 | 9 |
| 8 | 5 | Colin Edwards | Camel Yamaha Team | 07:41:17 | 24 | 8 | 10 |
| 9 | 10 | Kenny Jr Roberts | Team Roberts | 08:53:29 | 24 | 7 | 14 |
| 10 | 6 | Makoto Tamada | Konica Minolta Honda | 10:02:35 | 24 | 6 | 18 |
| 11 | 71 | Chris Vermeulen | Team Suzuki MotoGP | 12:20:48 | 24 | 5 | 15 |
| 12 | 21 | John Hopkins | Team Suzuki MotoGP | 12:23:45 | 24 | 4 | 13 |
| 13 | 64 | Kousuke Akiyoshi | Team Suzuki MotoGP | 14:06:20 | 24 | 3 | 12 |
| 14 | 7 | Carlos Checa | Tech3 Yamaha | 15:12:36 | 24 | 2 | 17 |
| 15 | 77 | James Ellison | Tech3 Yamaha | 20:37:50 | 24 | 1 | 19 |
| 16 | 66 | Alexander Hofmann | Pramac d\'Antin MotoGP | 21:22:13 | 24 | 0 | 20 |
| 17 | 56 | Shinya Nakano | Kawasaki Racing Team | 21:57:35 | 23 | 0 | 4 |
| 18 | 27 | Casey Stoner | Lcr Honda | 04:26:20 | 12 | 0 | 11 |
| 19 | 8 | Naoki Matsudo | Kawasaki Racing Team | 08:38:35 | 8 | 0 | 16 |
| 20 | 17 | Randy De Puniet | Kawasaki Racing Team | 04:56:03 | 8 | 0 | 8 |
| 21 | 30 | Jose Luis Cardoso | Pramac d\'Antin MotoGP | 10:37:00 | 1 | 0 | 21 |