The Australian topped the timesheet by a clear 0.263s, with a best lap of 1’32.256 securing him the lead on the front row of the grid.
Repsol Honda’s Dani Pedrosa was next quickest as he improved his own best practice time by over 0.4s to secure second place, ahead of Jorge Lorenzo.
Lorenzo, who was third fastest overall in the practice sessions, was not far behind with a margin of just 0.018s separating him from his fellow Spaniard.
Heading up the second row of the grid will be Lorenzo’s Fiat Yamaha team-mate and World Champion Valentino Rossi, whose fourth position was enough to secure him the BMW M Award for best qualifier in MotoGP in 2009.
Colin Edwards (Monster Yamaha Tech 3) secured fifth spot for the eighth time this season, after improving significantly on his own practice times from earlier in the weekend.
Stoner’s Ducati Marlboro team-mate Nicky Hayden took the final second-row slot with his final lap, beating Randy de Puniet (LCR Honda) to sixth.
De Puniet recovered from an early crash to ensure seventh place, after an impressive showing in both practice sessions carried over, whilst Toni Elías (San Carlo Honda Gresini) will occupy eighth in the starting positions.
Ben Spies, riding as a wildcard entry for the Sterilgarda Yamaha Team and completing only his fourth ever qualifying session in MotoGP, will line up ninth, with Andrea Dovizioso also coming inside the top ten times.