| Fecha 2 | A la Fecha 2 | |||||||||
| GRAND PRIX OF JAPAN | World Championship | |||||||||
| Pos. | Rider | Nation | Team | Total time | Pos. | Rider | Nation | Team | Points | |
| 1 | A. BAUTISTA | SPA | Mapfre Aspar Team | 44'06.488 | 1 | Alvaro BAUTISTA | SPA | Mapfre Aspar Team | 34 | |
| 2 | H. AOYAMA | JPN | Scot Racing Team 250cc | 5.889 | 2 | Hiroshi AOYAMA | JPN | Scot Racing Team 250cc | 33 | |
| 3 | M. PASINI | ITA | Team Toth Aprilia | 21.832 | 3 | Hector BARBERA | SPA | Pepe World Team | 30 | |
| 4 | G. TALMACSI | HUN | Balatonring Team | 25.906 | 4 | Jules CLUZEL | FRA | Matteoni Racing | 20 | |
| 5 | A. DEBON | SPA | Aeropuerto-Castello-Blusen | 30.785 | 5 | Gabor TALMACSI | HUN | Balatonring Team | 19 | |
| 6 | S. AOYAMA | JPN | Harc-Pro | 33.788 | 6 | Thomas LUTHI | SWI | Emmi - Caffe Latte | 18 | |
| 7 | L. PESEK | CZE | Auto Kelly - CP | 36.972 | 7 | Mattia PASINI | ITA | Team Toth Aprilia | 16 | |
| 8 | T. LUTHI | SWI | Emmi - Caffe Latte | 41.018 | 8 | Mike DI MEGLIO | FRA | Mapfre Aspar Team 250cc | 16 | |
| 9 | K. ABRAHAM | CZE | Cardion AB Motoracing | 41.649 | 9 | Raffaele DE ROSA | ITA | Scot Racing Team 250cc | 15 | |
| 10 | S. TOMIZAWA | JPN | CIP Moto - GP250 | 52.863 | 10 | Alex DEBON | SPA | Aeropuerto-Castello-Blusens | 13 | |
| 11 | H. BARBERA | SPA | Pepe World Team | + 1'00.888 | 11 | Lukas PESEK | CZE | Auto Kelly - CP | 12 | |
| 12 | R. DE ROSA | ITA | Scot Racing Team 250cc | + 1'06.347 | 12 | Shuhei AOYAMA | JPN | Harc-Pro | 10 | |
| 13 | I. TOTH | HUN | Team Toth Aprilia | + 1'53.149 | 13 | Shoya TOMIZAWA | JPN | CIP Moto - GP250 | 10 | |
| 14 | K. WATANABE | JPN | Bardral Racing with SJ-R | 1 Lap | 14 | Ratthapark WILAIROT | THA | Thai Honda PTT SAG | 8 | |
| 15 | V. LEONOV | RUS | Viessmann Kiefer Racing | 1 Lap | 15 | Karel ABRAHAM | CZE | Cardion AB Motoracing | 7 | |
| 16 | Roberto LOCATELLI | ITA | Metis Gilera | 7 | ||||||
| 17 | Hector FAUBEL | SPA | Valencia CF - Honda SAG | 5 | ||||||
| 18 | Imre TOTH | HUN | Team Toth Aprilia | 3 | ||||||
| 19 | Kazuki WATANABE | JPN | Bardral Racing with SJ-R | 2 | ||||||
| 20 | Vladimir LEONOV | RUS | Viessmann Kiefer Racing | 1 | ||||||
| 21 | Alex BALDOLINI | ITA | WTR San Marino Team | 1 | ||||||