Stoner earned the 41st pole position of his career — his 37th in Moto GP — by a margin of 115 thousandths of a second from Spanish teammate Dani Pedrosa.
Another Spaniard, Jorge Lorenzo, was third fastest in a session that was twice stopped because of the rain falling on the track.
Pedrosa had posted the quickest lap ahead of Lorenzo and Italy’s Andrea Dovizioso before the riders were forced inside for the first time on the day.
Stoner currently sits second in the overall standings, 25 points behind championship leader Lorenzo.
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