Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 3 | Max Biaggi | Camel Pramac Pons | 13:39:50 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Repsol Honda Team | 14:42:24 | 24 | 20 | 3 |
| 3 | 69 | Nicky Hayden | Repsol Honda Team | 15:13:51 | 24 | 16 | 5 |
| 4 | 15 | Sete Gibernau | Telefonica Movistar Honda | 19:04:06 | 24 | 13 | 4 |
| 5 | 33 | Marco Melandri | Fortuna Yamaha MotoGP | 19:11:39 | 24 | 11 | 9 |
| 6 | 4 | Alex Barros | Gauloises Yamaha Team | 19:28:48 | 24 | 10 | 8 |
| 7 | 11 | Tohru Ukawa | Camel Pramac Pons | 19:51:37 | 24 | 9 | 11 |
| 8 | 65 | Loris Capirossi | Ducati Marlboro Team | 21:24:37 | 24 | 8 | 6 |
| 9 | 56 | Shinya Nakano | D\'antin MotoGP | 01:15:21 | 24 | 7 | 12 |
| 10 | 43 | Akira Ryo | Team Suzuki MotoGP | 03:34:56 | 24 | 6 | 14 |
| 11 | 23 | Ryuichi Kiyonari | Telefonica Movistar Honda | 04:26:44 | 24 | 5 | 20 |
| 12 | 41 | Noriyuki Haga | Alice Aprilia Racing | 04:32:59 | 24 | 4 | 25 |
| 13 | 19 | Olivier Jacque | Gauloises Yamaha Team | 07:53:30 | 24 | 3 | 15 |
| 14 | 9 | Nobuatsu Aoki | Proton Team KR | 08:25:25 | 24 | 2 | 18 |
| 15 | 10 | Kenny Jr Roberts | Suzuki Grand Prix Team | 08:50:45 | 24 | 1 | 19 |
| 16 | 88 | Andrew Pitt | Kawasaki Racing Team | 09:32:03 | 24 | 0 | 22 |
| 17 | 45 | Colin Edwards | Alice Aprilia Racing | 13:59:33 | 24 | 0 | 13 |
| 18 | 25 | Tamaki Serizawa | Moriwaki Racing | 15:29:51 | 24 | 0 | 23 |
| 19 | 52 | David De Gea | WCM | 19:45:02 | 23 | 0 | 24 |
| 20 | 8 | Garry McCoy | Kawasaki Racing Team | 05:05:34 | 10 | 0 | 21 |
| 21 | 99 | Jeremy McWilliams | Proton Team KR | 17:14:37 | 2 | 0 | 17 |
| 22 | 35 | Chris Burns | WCM | 11:08:42 | 1 | 0 | 26 |
| 23 | 6 | Makoto Tamada | Pramac Racing | 01:00:00 | 0 | 0 | 2 |
| 24 | 7 | Carlos Checa | Fortuna Yamaha MotoGP | 01:00:00 | 0 | 0 | 7 |
| 25 | 12 | Troy Bayliss | Ducati Marlboro Team | 01:00:00 | 0 | 0 | 10 |
| 26 | 21 | John Hopkins | Suzuki Grand Prix Team | 01:00:00 | 0 | 0 | 16 |