The Repsol Honda man was consistently quicker than his rivals after getting to grips with the new surface at the Brickyard, which took some getting used to and saw times rapidly improving throughout.
Stoner looked sharp in free practice and built on that in qualifying this afternoon to finish 0.523 seconds clear of his nearest rival. Only two men actually produced laps within a second of the Australian.
Ben Spies took second on his home track on his Factory Yamaha to edge team-mate Jorge Lorenzo, the defending champion, by 0.256secs.
Lorenzo had struggled in practice but showed significant improvement.
Repsol Honda's Dani Pedrosa will set off from fourth, ahead of Andrea Dovizioso and Colin Edwards.
Valentino Rossi had a lowside fall early on and could only claw his way up to 14th.