Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 65 | Loris Capirossi | Ducati Marlboro Team | 47'05.484 | 24 | 25 | 8 |
| 2 | 14 | Randy De Puniet | Kawasaki Racing Team | 47'16.337 | 24 | 20 | 4 |
| 3 | 24 | Toni Elias | San Carlo Honda Gresini | 47'17.010 | 24 | 16 | 5 |
| 4 | 50 | Sylvain Guintoli | Tech3 Yamaha | 47'17.676 | 24 | 13 | 18 |
| 5 | 33 | Marco Melandri | San Carlo Honda Gresini | 47'34.053 | 24 | 11 | 10 |
| 6 | 27 | Casey Stoner | Ducati Marlboro Team | 47'36.663 | 24 | 10 | 9 |
| 7 | 13 | Anthony West | Kawasaki Racing Team | 47'55.485 | 24 | 9 | 6 |
| 8 | 4 | Alex Barros | Pramac d\'Antin | 47'57.827 | 24 | 8 | 15 |
| 9 | 1 | Nicky Hayden | Repsol Honda Team | 47'59.113 | 24 | 7 | 3 |
| 10 | 21 | John Hopkins | Rizla Suzuki MotoGP | 48'05.199 | 24 | 6 | 11 |
| 11 | 71 | Chris Vermeulen | Rizla Suzuki MotoGP | 48'08.288 | 24 | 5 | 17 |
| 12 | 6 | Makoto Tamada | Tech3 Yamaha | 48'14.797 | 24 | 4 | 16 |
| 13 | 46 | Valentino Rossi | Fiat Yamaha Team | 48'15.183 | 24 | 3 | 2 |
| 14 | 5 | Colin Edwards | Fiat Yamaha Team | 48'17.219 | 24 | 2 | 7 |
| 15 | 72 | Shinichi Itoh | Pramac d\'Antin | 48'17.774 | 24 | 1 | 20 |
| 16 | 56 | Shinya Nakano | Konica Minolta Honda | 48'38.463 | 24 | 0 | 12 |
| 17 | 87 | Akira Yanagawa | Kawasaki Racing Team | 47'34.190 | 23 | 0 | 19 |
| 18 | 7 | Carlos Checa | LCR Honda MotoGP | 48'03.727 | 23 | 0 | 14 |
| 19 | 64 | Kousuke Akiyoshi | Rizla Suzuki MotoGP | 40'07.818 | 20 | 0 | 13 |
| 20 | 26 | Dani Pedrosa | Repsol Honda Team | 28'09.647 | 14 | 0 | 1 |
| 21 | 80 | Kurtis Roberts | Team Roberts | 2'47.984 | 1 | 0 | 21 |