Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 3 | Max Biaggi | Camel Pramac Pons | 43'57.590 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Repsol Honda Team | 44'01.344 | 24 | 20 | 3 |
| 3 | 69 | Nicky Hayden | Repsol Honda Team | 44'03.231 | 24 | 16 | 5 |
| 4 | 15 | Sete Gibernau | Telefonica Movistar Honda | 44'17.046 | 24 | 13 | 4 |
| 5 | 33 | Marco Melandri | Fortuna Yamaha MotoGP | 44'17.499 | 24 | 11 | 9 |
| 6 | 4 | Alex Barros | Gauloises Yamaha Team | 44'18.528 | 24 | 10 | 8 |
| 7 | 11 | Tohru Ukawa | Camel Pramac Pons | 44'19.897 | 24 | 9 | 11 |
| 8 | 65 | Loris Capirossi | Ducati Marlboro Team | 44'25.477 | 24 | 8 | 6 |
| 9 | 56 | Shinya Nakano | D\'antin MotoGP | 44'39.321 | 24 | 7 | 12 |
| 10 | 43 | Akira Ryo | Team Suzuki MotoGP | 44'47.696 | 24 | 6 | 14 |
| 11 | 23 | Ryuichi Kiyonari | Telefonica Movistar Honda | 44'50.804 | 24 | 5 | 20 |
| 12 | 41 | Noriyuki Haga | Alice Aprilia Racing | 44'51.179 | 24 | 4 | 25 |
| 13 | 19 | Olivier Jacque | Gauloises Yamaha Team | 45'03.210 | 24 | 3 | 15 |
| 14 | 9 | Nobuatsu Aoki | Proton Team KR | 45'05.125 | 24 | 2 | 18 |
| 15 | 10 | Kenny Jr Roberts | Suzuki Grand Prix Team | 45'06.645 | 24 | 1 | 19 |
| 16 | 88 | Andrew Pitt | Kawasaki Racing Team | 45'09.123 | 24 | 0 | 22 |
| 17 | 45 | Colin Edwards | Alice Aprilia Racing | 45'25.173 | 24 | 0 | 13 |
| 18 | 25 | Tamaki Serizawa | Moriwaki Racing | 45'30.591 | 24 | 0 | 23 |
| 19 | 52 | David De Gea | WCM | 44'19.502 | 23 | 0 | 24 |
| 20 | 8 | Garry McCoy | Kawasaki Racing Team | 18'57.934 | 10 | 0 | 21 |
| 21 | 99 | Jeremy McWilliams | Proton Team KR | 3'51.277 | 2 | 0 | 17 |
| 22 | 35 | Chris Burns | WCM | 2'02.922 | 1 | 0 | 26 |
| 23 | 6 | Makoto Tamada | Pramac Racing | 0 | 0 | 2 | |
| 24 | 7 | Carlos Checa | Fortuna Yamaha MotoGP | 0 | 0 | 7 | |
| 25 | 12 | Troy Bayliss | Ducati Marlboro Team | 0 | 0 | 10 | |
| 26 | 21 | John Hopkins | Suzuki Grand Prix Team | 0 | 0 | 16 |