Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 65 | Loris Capirossi | Ducati Marlboro Team | 43'13.585 | 24 | 25 | 1 |
| 2 | 46 | Valentino Rossi | Fiat Yamaha Team | 43'18.673 | 24 | 20 | 2 |
| 3 | 33 | Marco Melandri | Fortuna Honda | 43'21.963 | 24 | 16 | 3 |
| 4 | 15 | Sete Gibernau | Ducati Marlboro Team | 43'23.297 | 24 | 13 | 5 |
| 5 | 69 | Nicky Hayden | Repsol Honda Team | 43'25.529 | 24 | 11 | 7 |
| 6 | 24 | Toni Elias | Fortuna Honda | 43'31.693 | 24 | 10 | 6 |
| 7 | 26 | Dani Pedrosa | Repsol Honda Team | 43'33.522 | 24 | 9 | 9 |
| 8 | 5 | Colin Edwards | Camel Yamaha Team | 43'36.077 | 24 | 8 | 10 |
| 9 | 10 | Kenny Jr Roberts | Team Roberts | 43'40.409 | 24 | 7 | 14 |
| 10 | 6 | Makoto Tamada | Konica Minolta Honda | 43'44.555 | 24 | 6 | 18 |
| 11 | 71 | Chris Vermeulen | Team Suzuki MotoGP | 43'52.848 | 24 | 5 | 15 |
| 12 | 21 | John Hopkins | Team Suzuki MotoGP | 43'53.025 | 24 | 4 | 13 |
| 13 | 64 | Kousuke Akiyoshi | Team Suzuki MotoGP | 43'59.180 | 24 | 3 | 12 |
| 14 | 7 | Carlos Checa | Tech3 Yamaha | 44'03.156 | 24 | 2 | 17 |
| 15 | 77 | James Ellison | Tech3 Yamaha | 44'22.670 | 24 | 1 | 19 |
| 16 | 66 | Alexander Hofmann | Pramac d\'Antin MotoGP | 44'25.333 | 24 | 0 | 20 |
| 17 | 56 | Shinya Nakano | Kawasaki Racing Team | 41'34.655 | 23 | 0 | 4 |
| 18 | 27 | Casey Stoner | Lcr Honda | 21'48.380 | 12 | 0 | 11 |
| 19 | 8 | Naoki Matsudo | Kawasaki Racing Team | 14'51.515 | 8 | 0 | 16 |
| 20 | 17 | Randy De Puniet | Kawasaki Racing Team | 14'38.163 | 8 | 0 | 8 |
| 21 | 30 | Jose Luis Cardoso | Pramac d\'Antin MotoGP | 2'01.020 | 1 | 0 | 21 |