The Australian suffered ligament damage and small fractures to his right ankle in a violent high side on the exit of Turn 13 early on in qualifying.
After checks in hospital, the Australian arrived at the circuit with his ankle in a cast, unable to put weight on it. The circuit's medical staff were satisfied with his mobility however, and with a modified race boot he headed out for the official warm up session, which he ended in sixth position.
Stoner confirmed shortly after that he felt comfortable enough to compete in the race.
He will be given an injection one hour before the race to dull the pain and allow him to last the 45 minutes. The Australian will line up sixth on the grid.
Yamaha's Ben Spies, who also fell heavily in qualifying, was the fastest rider in the warm up.
Nicky Hayden, another who crashed heavily in qualifying, will meanwhile miss out.