Stoner rode his Honda around the 5-kilometer (3-mile) MotorLand Aragon Circuit in 1 minute, 48.451 seconds.

Dani Pedrosa of Spain will start Sunday's race second on the grid with Ben Spies of the United States third.

Valentino Rossi continued his difficult season by crashing early in the session. The seven-time MotoGP champion returned to finish in 13th place.

Lorenzo was pessimistic about his chances for a win.

"We have many problems with the rear grip, we are not getting enough traction to be really fast," the Spanish rider said. "Tomorrow I think the maximum we can get is third place on the podium unless something very strange happens, so that is the goal we have." Stoner, who won last year's Aragon GP starting from pole, leads Lorenzo by 35 points in the overall standings with five races to go.

In the Moto2 category, Marc Marquez won the pole with a fastest lap of 1:53.296, while fellow Spaniard Julian Simon was second. Britain's Scott Redding was third.

In the 125cc class, Hector Faubel earned his first pole of the season after setting a track record of 1:59.222. Maverick Vinales and Nicolas Terol completed a Spanish sweep of the top three spots.