Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 6 | Makoto Tamada | Camel Honda | 43'43.220 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Gauloises Fortuna Yamaha | 43'49.388 | 24 | 20 | 3 |
| 3 | 56 | Shinya Nakano | Kawasaki Racing Team | 43'56.616 | 24 | 16 | 12 |
| 4 | 4 | Alex Barros | Repsol Honda Team | 43'58.655 | 24 | 13 | 10 |
| 5 | 33 | Marco Melandri | Fortuna Gauloises Tech 3 | 44'06.797 | 24 | 11 | 6 |
| 6 | 15 | Sete Gibernau | Telefonica Movistar Honda | 44'10.598 | 24 | 10 | 13 |
| 7 | 7 | Carlos Checa | Gauloises Fortuna Yamaha | 44'19.054 | 24 | 9 | 11 |
| 8 | 50 | Neil Hodgson | D\'antin MotoGP | 44'31.196 | 24 | 8 | 17 |
| 9 | 11 | Ruben Xaus | D\'antin MotoGP | 44'33.101 | 24 | 7 | 18 |
| 10 | 66 | Alexander Hofmann | Kawasaki Racing Team | 44'39.327 | 24 | 6 | 19 |
| 11 | 19 | Olivier Jacque | Moriwaki Racing | 45'04.457 | 24 | 5 | 21 |
| 12 | 99 | Jeremy McWilliams | MS Aprilia Racing | 45'10.903 | 24 | 4 | 20 |
| 13 | 67 | Shane Byrne | MS Aprilia Racing | 43'49.679 | 23 | 3 | 23 |
| 14 | 9 | Nobuatsu Aoki | Project U FRS | 44'09.067 | 23 | 2 | 22 |
| 15 | 41 | Youichi Iu | WCM | 45'35.870 | 23 | 1 | 24 |
| 16 | 12 | Troy Bayliss | Ducati Marlboro Team | 34'50.308 | 19 | 0 | 16 |
| 17 | 17 | Norifumi Abe | Fortuna Gauloises Tech 3 | 16'30.965 | 9 | 0 | 15 |
| 18 | 72 | Tohru Ukawa | HRC | 14'45.557 | 8 | 0 | 14 |
| 19 | 21 | John Hopkins | Team Suzuki MotoGP | 0 | 0 | 2 | |
| 20 | 3 | Max Biaggi | Camel Honda | 0 | 0 | 4 | |
| 21 | 45 | Colin Edwards | Telefonica Movistar Honda | 0 | 0 | 5 | |
| 22 | 65 | Loris Capirossi | Ducati Marlboro Team | 0 | 0 | 7 | |
| 23 | 10 | Kenny Jr Roberts | Team Suzuki MotoGP | 0 | 0 | 8 | |
| 24 | 69 | Nicky Hayden | Repsol Honda Team | 0 | 0 | 9 |