Texan Colin Edwards rode to a lonely eighth for Monster Yamaha Tech 3, with Hector Barbera ninth for Aspar Ducati. Hiroshi Aoyama snatched tenth from rookie Karel Abraham (Cardion AB), with Loris Capirossi (Pramac Ducati) and Toni Elias (LCR Honda) the last of the finishers.
Capirossi's team-mate Randy de Puniet, injured in qualifying, withdrew from event on Sunday morning, while Suzuki's Alvaro Bautista and Tech 3's Cal Crutchlow joined Simoncelli in crashing out.
Wild-card Ben Bostrom retired from his first MotoGP event, the 37-year-old pitting his LCR Honda just before the halfway stage after running off track several times.
The Factory Yamaha team were riding in special red-and-white livery for the second time this season, continuing their 50th anniversary of grand prix road racing celebrations.
MotoGP now heads for a two-weekend summer break before the Czech Republic Grand Prix, at Brno on August 12-14.
US Grand Prix: