Stoner on his Repsol Honda left it to the final moments to snatch first on the grid ahead Yamaha's BenSpies and his own teammate Dani Pedrosa of Spain.
The Spaniard failed to qualify on the front row of the grid at the circuit for the first time in his career, with Yamaha's 2010 world champion finishing fourth fastest ahead of American teammate BenSpies and San Carlo Honda Gresini's Alvaro Bautista.