Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 6 | Makoto Tamada | Camel Honda | 09:40:20 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Gauloises Fortuna Yamaha | 11:23:08 | 24 | 20 | 3 |
| 3 | 56 | Shinya Nakano | Kawasaki Racing Team | 13:23:36 | 24 | 16 | 12 |
| 4 | 4 | Alex Barros | Repsol Honda Team | 13:57:35 | 24 | 13 | 10 |
| 5 | 33 | Marco Melandri | Fortuna Gauloises Tech 3 | 16:13:17 | 24 | 11 | 6 |
| 6 | 15 | Sete Gibernau | Telefonica Movistar Honda | 17:16:38 | 24 | 10 | 13 |
| 7 | 7 | Carlos Checa | Gauloises Fortuna Yamaha | 19:37:34 | 24 | 9 | 11 |
| 8 | 50 | Neil Hodgson | D\'antin MotoGP | 22:59:56 | 24 | 8 | 17 |
| 9 | 11 | Ruben Xaus | D\'antin MotoGP | 23:31:41 | 24 | 7 | 18 |
| 10 | 66 | Alexander Hofmann | Kawasaki Racing Team | 01:15:27 | 24 | 6 | 19 |
| 11 | 19 | Olivier Jacque | Moriwaki Racing | 08:14:17 | 24 | 5 | 21 |
| 12 | 99 | Jeremy McWilliams | MS Aprilia Racing | 10:01:43 | 24 | 4 | 20 |
| 13 | 67 | Shane Byrne | MS Aprilia Racing | 11:27:59 | 23 | 3 | 23 |
| 14 | 9 | Nobuatsu Aoki | Project U FRS | 16:51:07 | 23 | 2 | 22 |
| 15 | 41 | Youichi Iu | WCM | 16:57:50 | 23 | 1 | 24 |
| 16 | 12 | Troy Bayliss | Ducati Marlboro Team | 05:38:28 | 19 | 0 | 16 |
| 17 | 17 | Norifumi Abe | Fortuna Gauloises Tech 3 | 12:16:05 | 9 | 0 | 15 |
| 18 | 72 | Tohru Ukawa | HRC | 06:59:17 | 8 | 0 | 14 |
| 19 | 21 | John Hopkins | Team Suzuki MotoGP | 01:00:00 | 0 | 0 | 2 |
| 20 | 3 | Max Biaggi | Camel Honda | 01:00:00 | 0 | 0 | 4 |
| 21 | 45 | Colin Edwards | Telefonica Movistar Honda | 01:00:00 | 0 | 0 | 5 |
| 22 | 65 | Loris Capirossi | Ducati Marlboro Team | 01:00:00 | 0 | 0 | 7 |
| 23 | 10 | Kenny Jr Roberts | Team Suzuki MotoGP | 01:00:00 | 0 | 0 | 8 |
| 24 | 69 | Nicky Hayden | Repsol Honda Team | 01:00:00 | 0 | 0 | 9 |