The Antipodean, chasing reigning champion Jorge Lorenzo's title, secured his fourth consecutive pole on the track with a best time of one minute 29.975 seconds to ensure he will start ahead of the Spaniard, who was 0.473secs off.
Lorenzo will at least have reason for optimism as he starts next to Stoner on the front row, while the Australian needs him to finish outside the top three.
Stoner came off in the first practice session on Friday but recovered to top the timesheets in both morning and afternoon. The Australian Repsol Honda rider needs to outscore Lorenzo by 10 points on Sunday to take the title in a race he has won four times in a row.
Factory Yamaha man Lorenzo was followed by Stoner's Honda team-mate Marco Simoncelli (0.624secs), who came on strong to edge Suzuki's Alvaro Bautista.
Dani Pedrosa laboured to start in eighth position behind American Ben Spies in seventh.
Former champion Valentino Rossi came home 13th quickest.
"So far so good. We have a good race pace and the bike's feeling pretty good at the moment. We still need to improve the rear grip, but I think this is the same for everyone," Stoner said afterwards.
"We'd also like to get the harder rear tyre working better for the race.
"We began qualifying with older tyres to understand where we are for the race and I'm quite happy, as the lap times we were achieving were similar to Jorge (Lorenzo) and Dani (Pedrosa), who were on the new soft tyre."