Japanese Grand Prix
| Pos | Num. | Rider | Nation | Team | Bike | Time/Gap |
| 1 | 27 | Casey STONER | AUS | Ducati Team | Ducati | 43’12.266 |
| 2 | 4 | Andrea DOVIZIOSO | ITA | Repsol Honda Team | Honda | +3.868 |
| 3 | 46 | Valentino ROSSI | ITA | Fiat Yamaha Team | Yamaha | +5.707 |
| 4 | 99 | Jorge LORENZO | SPA | Fiat Yamaha Team | Yamaha | +6.221 |
| 5 | 5 | Colin EDWARDS | USA | Monster Yamaha Tech 3 | Yamaha | +27.092 |
| 6 | 58 | Marco SIMONCELLI | ITA | San Carlo Honda Gresini | Honda | +30.021 |
| 7 | 19 | Alvaro BAUTISTA | SPA | Rizla Suzuki MotoGP | Suzuki | +31.826 |
| 8 | 11 | Ben SPIES | USA | Monster Yamaha Tech 3 | Yamaha | +35.572 |
| 9 | 14 | Randy DE PUNIET | FRA | LCR Honda MotoGP | Honda | +47.564 |
| 10 | 7 | Hiroshi AOYAMA | JPN | Interwetten Honda MotoGP | Honda | +49.598 |
| 11 | 33 | Marco MELANDRI | ITA | San Carlo Honda Gresini | Honda | +49.999 |
| 12 | 69 | Nicky HAYDEN | USA | Ducati Team | Ducati | +50.703 |
| 13 | 40 | Hector BARBERA | SPA | Paginas Amarillas Aspar | Ducati | +51.422 |
| 14 | 41 | Aleix ESPARGARO | SPA | Pramac Racing Team | Ducati | +52.843 |
| 15 | 36 | Mika KALLIO | FIN | Pramac Racing Team | Ducati | +1’14.668 |
| 65 | Loris CAPIROSSI | ITA | Rizla Suzuki MotoGP | Suzuki | 3 Laps |