Yamaha's championship leader Jorge Lorenzo was the only rider able to get within one second of the Australian, while the session's two slowest riders were outside the 107 per cent mark.
The Australian, who admitted his injuries had worsened coming into his home track, wasted little time getting up to speed.
Within four laps he had got down to a 1m31.046s, which itself would have been good enough to seal top spot.
After Honda team-mate Dani Pedrosa and then Lorenzo got close to that benchmark in the final 10 minutes however he shaved more than half a second off his previous best, ending with a 1m30.374s.
Lorenzo and Pedrosa were left trailing as a result, while the rest of the field were more than 1.5s in arrears.
Tech 3's Andrea Dovizioso was fourth fastest ahead of Gresini's Andrea Bautista and team-mate Cal Crutchlow, struggling with bronchitis and fever this weekend.
Ducati's Nicky Hayden and Valentino Rossi then occupied seventh and ninth, sandwiching the LCR Honda of Stefan Bradl.
Rossi, like Stoner a five-time winner at the circuit, was 2.2s down on the overall pace.
Alongside a short shower around the halfway mark, which led to a temporary lull in proceedings, there were precious few incidents.
Pedrosa almost suffered a massive highside however, as Crutchlow - only yards ahead on the circuit - hit a wet patch with his knee, flicking up a spray which surprised Pedrosa and forced him to snatch at his bike, causing a wobble he was ultimately able to save.
The incident followed moments after Gresini's Michele Pirro, confirmed as Ducati's official test rider next year, suffered his own highside exiting Honda hairpin. He was able to hold on but veered off track and went down in the grass.