2006 Malaysian motorcycle Grand Prix MotoGP classification MotoGP classification

| Rider | Manufacturer | Laps | Time_Retired | Grid |
|---|---|---|---|---|
| Valentino Rossi | Yamaha | 21 | 43:07.829 | 1 |
| Sete Gibernau | Ducati | 21 | +0.849 | 3 |
| Dani Pedrosa | Honda | 21 | +3.863 | 19 |
| Nicky Hayden | Honda | 21 | +5.780 | 2 |
| Loris Capirossi | Ducati | 21 | +9.301 | 5 |
| John Hopkins | Suzuki | 21 | +11.081 | 7 |
| Kenny Roberts, Jr. | KR211V | 21 | +11.838 | 4 |
| Casey Stoner | Honda | 21 | +12.267 | 9 |
| Marco Melandri | Honda | 21 | +15.019 | 8 |
| Colin Edwards | Yamaha | 21 | +19.909 | 10 |
| Chris Vermeulen | Suzuki | 21 | +24.371 | 14 |
| Carlos Checa | Yamaha | 21 | +30.884 | 13 |
| Randy de Puniet | Kawasaki | 21 | +36.335 | 6 |
| Makoto Tamada | Honda | 21 | +48.777 | 15 |
| Alex Hofmann | Ducati | 21 | +59.081 | 16 |
| James Ellison | Yamaha | 21 | +1:05.787 | 17 |