The Australian took advantage of perfect conditions to edge out his Repsol Honda team-mate Dani Pedrosa, a three-time winner of the meeting, by 0.252 seconds to set the fastest time in qualifying practice.
Stoner, who leads the overall standings by 19 points from defending champion Jorge Lorenzo, sustained a fall in the second practice session yesterday but was clearly suffering no adverse affects as he clocked one minute 21.681 seconds.
Lorenzo's Factory Yamaha will start from third on the grid, while Marco Simoncelli (San Carlo Honda Gresini) qualified fourth having topped the timesheets yesterday.
Ben Spies (Yamaha Factory) was fifth and Andrea Dovizioso (Repsol Honda), third in the standings, was sixth quickest.
Colin Edwards (Monster Yamaha Tech 3), Nicky Hayden (Ducati), Randy De Puniet (Pramac Racing) and Alvaro Bautista (Rizla Suzuki) completed the top 10.
Pedrosa was racing in just his second event back since missing three races with a broken collarbone, and the Spaniard admitted that injury is still causing him problems.
"It still feels very recent and I still feel some weakness," Pedrosa said.
"At least this track has many left-handers, so it gives me a bit more rest on my right arm and lets me give more focus on my riding.
"The first part of the lap is always tight - especially at the start - so being near the front is very good."