Course disputée sur le circuit de Twin Ring Motegi
| Position | Numéro | Pilote | Team | Temps | Tours | Points | Départ |
|---|---|---|---|---|---|---|---|
| 1 | 26 | Dani Pedrosa | Repsol Honda Team | 42'31.569 | 24 | 25 | 2 |
| 2 | 99 | Jorge Lorenzo | Yamaha Factory Racing | 42'35.844 | 24 | 20 | 1 |
| 3 | 19 | Alvaro Bautista | Honda Gresini | 42'38.321 | 24 | 16 | 5 |
| 4 | 4 | Andrea Dovizioso | Tech3 Yamaha | 42'47.966 | 24 | 13 | 6 |
| 5 | 1 | Casey Stoner | Repsol Honda Team | 42'52.135 | 24 | 11 | 7 |
| 6 | 6 | Stefan Bradl | LCR Honda MotoGP | 42'56.136 | 24 | 10 | 8 |
| 7 | 46 | Valentino Rossi | Ducati Team | 42'57.641 | 24 | 9 | 9 |
| 8 | 69 | Nicky Hayden | Ducati Team | 43'08.293 | 24 | 8 | 10 |
| 9 | 21 | Katsuyuki Nakasuga | Yamaha Ysp Racing Team | 43'08.363 | 24 | 7 | 11 |
| 10 | 8 | Hector Barbera | Pramac Racing Team | 43'42.298 | 24 | 6 | 12 |
| 11 | 17 | Karel Abraham | Cardion AB Motoracing | 43'47.227 | 24 | 5 | 15 |
| 12 | 41 | Aleix Espargaro | Aspar Team MotoGP (CRT) | 43'54.338 | 24 | 4 | 13 |
| 13 | 5 | Colin Edwards | Forward Racing (CRT) | 43'56.537 | 24 | 3 | 16 |
| 14 | 77 | James Ellison | Paul Bird Racing (CRT) | 44'00.957 | 24 | 2 | 20 |
| 15 | 51 | Michele Pirro | Honda Gresini (CRT) | 44'06.181 | 24 | 1 | 18 |
| 16 | 84 | Roberto Rolfo | Speed Master | 44'22.422 | 24 | 0 | 21 |
| 17 | 9 | Danilo Petrucci | Ioda Racing Project (CRT) | 42'23.577 | 23 | 0 | 19 |
| 18 | 35 | Cal Crutchlow | Tech3 Yamaha | 40'52.384 | 23 | 0 | 3 |
| 19 | 14 | Randy De Puniet | Aspar Team MotoGP (CRT) | 26'18.639 | 14 | 0 | 14 |
| 20 | 22 | Ivan Silva | BQR (CRT) | 25'59.326 | 14 | 0 | 22 |
| 21 | 68 | Yonny Hernandez | BQR (CRT) | 1'57.956 | 1 | 0 | 17 |
| 22 | 11 | Ben Spies | Yamaha Factory Racing | 1'53.106 | 1 | 0 | 4 |