The Australian's quickest lap was one minute 21.681 seconds - 0.252 seconds ahead of Honda team-mate Dani Pedrosa.
It will be the sixth time this season that Stoner has started from the front of the grid, as he chases his fifth win.
Defending world champion Jorge Lorenzo completes the front row of the grid.
Marco Simoncelli of Italy, Ben Spies of the United States and Andrea Dovizioso of Italy will start from the second row.
It was a turnaround in fortunes for Stoner, who leads Lorenzo by 19 points in the standings but had lagged behind in Friday practice after suffering a crash in a morning run.
He said: "I'm very happy with the outcome. I wasn't too confident on the quick part of the track where I crashed but we have recovered a lot of time since Friday."
MotoGP qualifying result:
1. Casey Stoner (Aus) Honda, One minute 21.681 seconds
2. Dani Pedrosa (Sp) Honda, 1:21.933
3. Jorge Lorenzo (Sp) Yamaha, 1:21.944
4. Marco Simoncelli (It) Honda, 1:21.954
5. Ben Spies (US) Yamaha, 1:22.056
6. Andrea Dovizioso (It) Honda, 1:22.157
7. Colin Edwards (US) Yamaha, 1:22.368
8. Nicky Hayden (US) Ducati, 1:22.388
9. Randy De Puniet (Fra) Ducati, 1:22.503
10. Alvaro Bautista (Sp) Suzuki, 1:22.604
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