The Honda rider, champion in 2007, clocked one minute 48.034 seconds at the Mugello circuit to claim the 27th pole of his career and his fifth of the season.
American Ben Spies (Yamaha) and Italian Marco Simoncelli (Honda) will join the Australian on the front row of the grid for the eighth race of the year.
Stoner, who has won four races this season, was almost half a second faster than Spies who is racing at Mugello for only the second time. Simoncelli was edged into third spot by a hair's breadth.
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World champion Jorge Lorenzo, second in this year's series, will start in fifth place as he tries to add to his solitary win of the season in Spain while Italian great Valentino Rossi was 12th.
Rossi's compatriot Andrea Dovizioso, third in the championship, will start fourth on the grid.
Italian Loris Capirossi, 38, misses his home MotoGP for the first time in 20 years after fracturing two ribs last week.
Spaniard Dani Pedrosa, back after breaking his collarbone in a fall at the French Grand Prix last month, qualified in eighth place.
