The Australian, aggrieved at losing out on pole after being held up on Saturday, made his move with 11 laps remaining to out drag Lorenzo on the main straight and he was able to comfortably hold the Yamaha rider behind him until the chequered flag.
Andrea Dovizioso finished fourth ahead of Britain’s Cal Crutchlow after home favourite Ben Spies crashed out of fourth place on lap ten before the corkscrew, a broken suspension looking to blame. Two-time Laguna Seca winner Nicky Hayden was sixth.
Starting from pole position, Lorenzo made a great getaway to lead from Stoner, Pedrosa and Spies. Dovizioso got the jump on Crutchlow and further back there was contact between Randy De Puniet and Michele Pirro, the latter being forced to retire after sliding off.
The top three quickly established a gap of over 10 seconds to fourth placed Spies and it was always going to be a fight to the flag between the championship leader and the two Honda riders, Stoner gambling on the softer of the option compound tyres.
Stoner, who has vowed to retire at the end of the season, was able to extend his lead to over four seconds by the finish and was delighted at getting one over on his Spanish rival.
“It was tactical from the start we went on the softer option which nobody decided to go on so I wanted to go in front from the outset,” said Stoner afterwards. “I bided my time, hunted Jorge down and in the end went past.”
Seven time champion Valentino Rossi had a big accident with only two laps remaining his bike somersaulting into the sand before the corkscrew. He thankfully walked away unscathed.