| CLASIFICACIÓN FINAL |
| Mundial de MotoGP 2006 - GP de Japón |
| 125cc | 250cc | MotoGP |
| Pos. | Nombre |
Equipo |
Moto |
Tiempo |
|
| 1 | Loris Capirossi | Ducati Marlboro Team | Ducati | 43'13"585 | |
| 2 | Valentino Rossi | Camel Yamaha Team | Yamaha | + 05"088 | |
| 3 | Marco Melandri | Fortuna Honda | Honda | + 08"378 | |
| 4 | Sete Gibernau | Ducati Marlboro Team | Ducati | + 09"712 | |
| 5 | Nicky Hayden | Repsol Honda Team | Honda | + 11"944 | |
| 6 | Toni Elías | Fortuna Honda | Honda | + 18"108 | |
| 7 | Dani Pedrosa | Repsol Honda Team | Honda | + 19"937 | |
| 8 | Colin Edwards | Camel Yamaha Team | Yamaha | + 22"492 | |
| 9 | Kenny Roberts Jr. | Team Roberts | Proton KR | + 26"824 | |
| 10 | Makoto Tamada | Konica Minolta Honda | Honda | + 30"970 | |
| 11 | Chris Vermeulen | Rizla Suzuki MotoGP | Suzuki | + 39"263 | |
| 12 | John Hopkins | Rizla Suzuki MotoGP | Suzuki | + 39"440 | |
| 13 | Kousuke Akiyoshi | Rizla Suzuki MotoGP | Suzuki | + 45"595 | |
| 14 | Carlos Checa | Tech 3 Yamaha | Yamaha | + 49"571 | |
| 15 | James Ellison | Tech 3 Yamaha | Yamaha | + 01'09"085 | |
| 16 | Alex Hofmann | Ducati Marlboro Team | Ducati | + 01'11"748 | |