| Fecha 2 | A la Fecha 2 | |||||||||
| GRAND PRIX OF JAPAN | World Championship | |||||||||
| Pos. | Rider | Nation | Team | Total time | Pos. | Rider | Nation | Team | Points | |
| 1 | J. LORENZO | SPA | Fiat Yamaha Team | 43'47.238 | 1 | Jorge LORENZO | SPA | Fiat Yamaha Team | 41 | |
| 2 | V. ROSSI | ITA | Fiat Yamaha Team | 1.304 | 2 | Valentino ROSSI | ITA | Fiat Yamaha Team | 40 | |
| 3 | D. PEDROSA | SPA | Repsol Honda Team | 3.763 | 3 | Casey STONER | AUS | Ducati Marlboro Team | 38 | |
| 4 | C. STONER | AUS | Ducati Marlboro Team | 5.691 | 4 | Andrea DOVIZIOSO | ITA | Repsol Honda Team | 22 | |
| 5 | A. DOVIZIOSO | ITA | Repsol Honda Team | 9.207 | 5 | Dani PEDROSA | SPA | Repsol Honda Team | 21 | |
| 6 | M. MELANDRI | ITA | Hayate Racing Team | 30.555 | 6 | Colin EDWARDS | USA | Monster Yamaha Tech 3 | 17 | |
| 7 | L. CAPIROSSI | ITA | Rizla Suzuki MotoGP | 32.756 | 7 | Mika KALLIO | FIN | Pramac Racing | 16 | |
| 8 | M. KALLIO | FIN | Pramac Racing | 39.416 | 8 | Chris VERMEULEN | AUS | Rizla Suzuki MotoGP | 15 | |
| 9 | J. TOSELAND | GBR | Monster Yamaha Tech 3 | 43.106 | 9 | Alex DE ANGELIS | RSM | San Carlo Honda Gresini | 13 | |
| 10 | C. VERMEULEN | AUS | Rizla Suzuki MotoGP | 43.245 | 10 | Marco MELANDRI | ITA | Hayate Racing Team | 12 | |
| 11 | R. DE PUNIET | FRA | LCR Honda MotoGP | 44.834 | 11 | Randy DE PUNIET | FRA | LCR Honda MotoGP | 11 | |
| 12 | C. EDWARDS | USA | Monster Yamaha Tech 3 | 46.54 | 12 | Loris CAPIROSSI | ITA | Rizla Suzuki MotoGP | 9 | |
| 13 | A. DE ANGELIS | RSM | San Carlo Honda Gresini | 53.525 | 13 | Toni ELIAS | SPA | San Carlo Honda Gresini | 8 | |
| 14 | N. CANEPA | ITA | Pramac Racing | + 1'21.804 | 14 | James TOSELAND | GBR | Monster Yamaha Tech 3 | 7 | |
| 15 | T. ELIAS | SPA | San Carlo Honda Gresini | 1 Lap | 15 | Nicky HAYDEN | USA | Ducati Marlboro Team | 4 | |