Third Repsol Honda rider Andrea Dovizioso and Gresini Honda's Marco Simoncelli, also on a factory bike, slugged it out for almost the entire race before Dovizioso shook-off his fellow Italian for fourth in the closing stages.
Ben Spies dropped from fifth to eighth on lap one, and finished his factory Yamaha debut in sixth place after battling his predecessor Valentino Rossi for much of the race.
The Italian superstar began his first race for Ducati in ninth, concerned by both the strength of his healing shoulder and set-up of his Desmosedici, after a winter in which he had failed to trouble the leading Hondas and Yamahas.
But Rossi is famous for putting up a fight on race day, particularly when the odds are against him, and the seven time MotoGP champion made an instant impact in 'red' as he momentarily grabbed second into turn one.
It was an optimistic move, the angle of which inevitably sent Rossi wide, and he slotted back into sixth - a position he stubbornly defended from Spies.
Spies persistently ran wide when trying to pass Rossi into turn one, but the Italian had a scare on lap 16 as he tried desperately to keep the Texan at bay and he backed off thereafter.
Rossi eventually crossed the line in seventh, as the top Ducati, but was 16 seconds from Stoner and six seconds from Spies.
Experienced Americans Colin Edwards (Monster Yamaha Tech 3) and Nicky Hayden (Ducati Marlboro) were eighth and ninth, with Hiroshi Aoyama tenth on the second Gresini Honda.
Cal Crutchlow's first grand prix in any class saw the Tech 3 rider, who impressed by claiming eighth in qualifying despite pain from his injured finger, hold ninth in the early stages before slipping to twelfth.
The Englishman then finished his first race positively by overtaking Aspar Ducati's Hector Barbera on the very last lap.
Crutchlow's fellow rookie Karel Abraham (Cardion AB Ducati) was the 13th and final rider to see the chequered flag.
Both Pramac Ducatis failed to finish after some exceptional bad luck: Randy de Puniet highsided on the opening lap while trying to overtake team-mate Loris Capirossi, the Frenchman's bike then clipping Capirossi's hand and forcing him to retire soon after.
Toni Elias crashed out at far higher speed on lap 19, while 14th and last for LCR Honda.
All riders used the harder option front and rear tyre.
Suzuki's only 2011 MotoGP rider, Alvaro Bautista, missed the race after breaking his left femur in a Friday night highside. Former Suzuki MotoGP rider John Hopkins will ride in place of Bautista during round two, at Jerez from April 1-3.
Honda hasn't won the first race of the season since 2003, with Rossi.
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