Dani Pedrosa (Repsol Honda) secured his third victory of the season at the Twin Ring Motegi circuit in an eventful race that saw false starts and many riders venturing into the gravel.
The race started with Dovizioso jumping the start, leading Cal Crutchlow and Marco Simoncelli (San Carlo Honda Gresini Team) to follow suit, whilst Stoner made a strong start to take the lead.
Valentino Rossi had a disappointing start to the race, crashing out of the first lap and pushing Ben Spies (Yamaha Factory Racing) into the gravel. Spies was able to rejoin, whilst Rossi was forced to retire.
Stoner stretched a gap at the lead, looking set to maintain first until the Australian ran out of track on lap five. Héctor Barberá (Mapfre Aspar) then crashed out and Nicky Hayden (Ducati Team) lost fifth place after running off the track and dropping back to tenth.
Damian Cudlin crashed out of fourteenth and Bautista then crashed out of fourth on lap fourteen before Elias crashed out of sixth.
Pedrosa maintained the lead to take the win and Lorenzo took second, with the pair the only riders in the top seven not to run off track or receive a ride through penalty for jumping the start, whilst Stoner managed to secure third.
Simoncelli and Dovizioso took their ride through penalties before fighting for fourth. Simoncelli managed to hang on to fourth, with Dovizioso being made to settle for fifth.
Spies recovered from his early trip in to the gravel to take sixth place, finishing ahead of fellow Americans Nicky Hayden and Colin Edwards who took seventh and eighth respectively.
Despite running off the track and being made to take a ride through penalty Cal Crutchlow finished in eleventh on his first trip to the Japanese circuit.
1. Dani PEDROSA SPA Repsol Honda Team Honda 161.6 42'47.481
2. Jorge LORENZO SPA Yamaha Factory Racing Yamaha 161.1 +7.299
3. Casey STONER AUS Repsol Honda Team Honda 160.4 +18.380
4. Marco SIMONCELLI ITA San Carlo Honda Gresini Honda 160.1 +23.550
5. Andrea DOVIZIOSO ITA Repsol Honda Team Honda 160.1 +23.691
6. Ben SPIES USA Yamaha Factory Racing Yamaha 159.2 +37.604
7. Nicky HAYDEN USA Ducati Team Ducati 159.1 +39.167
8. Colin EDWARDS USA Monster Yamaha Tech 3 Yamaha 158.8 +45.023
9. Hiroshi AOYAMA JPN San Carlo Honda Gresini Honda 158.5 +49.074
10. Randy DE PUNIET FRA Pramac Racing Team Ducati 157.9 +59.022
11. Cal CRUTCHLOW GBR Monster Yamaha Tech 3 Yamaha 157.0 +1'13.964
12. Kousuke AKIYOSHI JPN LCR Honda MotoGP Honda 156.6 +1'21.709
13. Shinichi ITO JPN Honda Racing Team Honda 156.3 +1'26.381
24 Toni ELIAS SPA LCR Honda MotoGP Honda 158.8 7 Laps
19 Alvaro BAUTISTA SPA Rizla Suzuki MotoGP Suzuki 159.7 11 Laps
6 Damian CUDLIN AUS Pramac Racing Team Ducati 156.7 11 Laps
8 Hector BARBERA SPA Mapfre Aspar Team MotoGP Ducati 147.6 23 Laps
46 Valentino ROSSI ITA Ducati Team Ducati 0 Lap