Casey Stoner overtook Ben Spies on the run to the finish line.
Alvaro Bautista, Valentino Rossi, Nicky Hayden and Randy de Puniet crashed out at the first turn.
Colin Edwards, injured in Marco Simoncelli's fatal accident at Sepang, was replaced by reigning AMA Superbike champion Josh Hayes.
Injured 2010 world champion Jorge Lorenzo was again being replaced by Yamaha test rider Katsuyuki Nakasuga. Loris Capirossi was riding with Simoncelli's #58 for his final grand prix appearance.
Today's race was the last of the 800cc era.
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1. Casey Stoner
AUS Repsol Honda 48m 18.645s
2. Ben Spies
USA Yamaha Factory Racing 48m 18.660s
3. Andrea Dovizioso
ITA Repsol Honda 48m 24.581s
4. Cal Crutchlow
GBR Monster Yamaha Tech 3 48m 27.363s
5. Dani Pedrosa
ESP Repsol Honda 48m 27.966s
6. Katsuyuki Nakasuga
JPN Yamaha Factory Racing 48m 42.463s
7. Josh Hayes
USA Monster Yamaha Tech 3 48m 51.763s
8. Karel Abraham
CZE Cardion AB Motoracing 48m 56.597s
9. Loris Capirossi
ITA Pramac Racing 49m 7.598s
10. Toni Elias
ESP LCR Honda 49m 11.146s
11. Hector Barbera
ESP Mapfre Aspar 49m 25.164s
12. Hiroshi Aoyama
JPN San Carlo Honda Gresini 49m 27.405s
Randy de Puniet
FRA Pramac Racing
USA Ducati Marlboro
ITA Ducati Marlboro
ESP Rizla Suzuki