Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 65 | Loris Capirossi | Ducati Marlboro Team | 43'30.499 | 24 | 25 | 1 |
| 2 | 3 | Max Biaggi | Honda Racing Corporation | 43'31.978 | 24 | 20 | 5 |
| 3 | 6 | Makoto Tamada | Konica Minolta Honda | 43'46.726 | 24 | 16 | 4 |
| 4 | 7 | Carlos Checa | Ducati Marlboro Team | 43'52.647 | 24 | 13 | 9 |
| 5 | 21 | John Hopkins | Team Suzuki MotoGP | 44'03.711 | 24 | 11 | 2 |
| 6 | 5 | Colin Edwards | Gauloise Yamaha | 44'05.414 | 24 | 10 | 13 |
| 7 | 69 | Nicky Hayden | Repsol Honda Team | 44'16.393 | 24 | 9 | 6 |
| 8 | 10 | Kenny Jr Roberts | Team Suzuki MotoGP | 44'26.997 | 24 | 8 | 8 |
| 9 | 24 | Toni Elias | Fortuna Yamaha MotoGP | 44'42.536 | 24 | 7 | 17 |
| 10 | 11 | Ruben Xaus | Fortuna Yamaha MotoGP | 45'05.426 | 24 | 6 | 19 |
| 11 | 27 | Franco Battaini | Blata WCM | 44'38.510 | 23 | 5 | 20 |
| 12 | 4 | Alex Barros | Camel Honda | 21'59.118 | 12 | 0 | 10 |
| 13 | 46 | Valentino Rossi | Gauloise Yamaha | 21'50.273 | 12 | 0 | 11 |
| 14 | 33 | Marco Melandri | Honda Gresini | 21'49.319 | 12 | 0 | 3 |
| 15 | 15 | Sete Gibernau | Honda Gresini | 20'08.260 | 11 | 0 | 7 |
| 16 | 56 | Shinya Nakano | Kawasaki Racing Team | 14'43.191 | 8 | 0 | 14 |
| 17 | 72 | Tohru Ukawa | Moriwaki Racing | 7'29.419 | 4 | 0 | 15 |
| 18 | 66 | Alexander Hofmann | Kawasaki Racing Team | 3'49.960 | 2 | 0 | 12 |
| 19 | 44 | Roberto Rolfo | Team d\'Antin Pramac | 3'49.595 | 2 | 0 | 16 |
| 20 | 45 | Naoki Matsudo | Moriwaki Racing | 0 | 0 | 18 |