Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 65 | Loris Capirossi | Ducati Marlboro Team | 17:51:24 | 24 | 25 | 8 |
| 2 | 14 | Randy De Puniet | Kawasaki Racing Team | 20:52:17 | 24 | 20 | 4 |
| 3 | 24 | Toni Elias | San Carlo Honda Gresini | 21:03:30 | 24 | 16 | 5 |
| 4 | 50 | Sylvain Guintoli | Tech3 Yamaha | 21:14:36 | 24 | 13 | 18 |
| 5 | 33 | Marco Melandri | San Carlo Honda Gresini | 01:47:33 | 24 | 11 | 10 |
| 6 | 27 | Casey Stoner | Ducati Marlboro Team | 02:31:03 | 24 | 10 | 9 |
| 7 | 13 | Anthony West | Kawasaki Racing Team | 07:44:45 | 24 | 9 | 6 |
| 8 | 4 | Alex Barros | Pramac d\'Antin | 08:23:47 | 24 | 8 | 15 |
| 9 | 1 | Nicky Hayden | Repsol Honda Team | 08:45:13 | 24 | 7 | 3 |
| 10 | 21 | John Hopkins | Rizla Suzuki MotoGP | 10:26:39 | 24 | 6 | 11 |
| 11 | 71 | Chris Vermeulen | Rizla Suzuki MotoGP | 11:18:08 | 24 | 5 | 17 |
| 12 | 6 | Makoto Tamada | Tech3 Yamaha | 13:06:37 | 24 | 4 | 16 |
| 13 | 46 | Valentino Rossi | Fiat Yamaha Team | 13:13:03 | 24 | 3 | 2 |
| 14 | 5 | Colin Edwards | Fiat Yamaha Team | 13:46:59 | 24 | 2 | 7 |
| 15 | 72 | Shinichi Itoh | Pramac d\'Antin | 13:56:14 | 24 | 1 | 20 |
| 16 | 56 | Shinya Nakano | Konica Minolta Honda | 19:41:03 | 24 | 0 | 12 |
| 17 | 87 | Akira Yanagawa | Kawasaki Racing Team | 01:49:50 | 23 | 0 | 19 |
| 18 | 7 | Carlos Checa | LCR Honda MotoGP | 10:02:07 | 23 | 0 | 14 |
| 19 | 64 | Kousuke Akiyoshi | Rizla Suzuki MotoGP | 21:50:18 | 20 | 0 | 13 |
| 20 | 26 | Dani Pedrosa | Repsol Honda Team | 14:20:47 | 14 | 0 | 1 |
| 21 | 80 | Kurtis Roberts | Team Roberts | 23:39:44 | 1 | 0 | 21 |