The 2007 champion had started on pole, having set a lap record in qualifying, and after briefly slipping down to third, he hit the front on the second lap and left the rest of the field trailing.
Spaniard Dani Pedrosa, Stoner's Repsol Honda team mate, claimed his third consecutive runner-up spot while defending champion Jorge Lorenzo was third on a Yamaha.
With four races left, championship leader Stoner extended his lead over second-placed Lorenzo to 44 points, climbing to 284.
"We had a difficult race in San Marino (when Stoner came third two weeks ago) but we knew the problem, that I was tired and that the bike was good enough," Stoner told Spanish television.
"But this weekend the bike's been good, I've been good and everything has been perfect." Stoner went on to say riders' worries about the fallout from the Fukushima nuclear disaster in March had been overcome ahead of the Sept. 30 Japanese Grand Prix.
"It looks like everything's going ahead for Japan," he said. "We found out as much information as we could and really there is no reason for us not to go there now. Three months ago it was a bit different, but I think everybody will be there." Under cloudy skies, with a gusting wind, Stoner and Pedrosa almost came together before the first bend at the MotorLand circuit and Ben Spies took advantage to nip into first place, but he did not hold on to it for long.
Stoner stormed back to take the lead and finished more than eight seconds ahead of Pedrosa, and 14 in front of Lorenzo.
"We passed from glory in the last race to being a long way off Stoner and Pedrosa today," Lorenzo said. "In the end this was the best result we were capable of." Earlier in the season, the Spaniard had also questioned the wisdom of going ahead with the Japan race but seemed to have changed his mind.
"In the end we are going," he said. "Let's hope the race doesn't go as badly as it did here." Italian Marco Simoncelli was fourth ahead of American Spies and Spaniard Alvaro Bautista.
Former champion Valentino Rossi came in tenth after being forced to start from the pit lane with a 10-second penalty for opting to use a seventh engine in the race. Riders are allowed only six per campaign.
Spaniard Marc Marquez won the Moto 2 race ahead of Italians Andrea Iannone and Simone Corsi with championship leader Stefan Bradl of Germany finishing eighth.
Another Spaniard, championship leader Nico Terol, won the 125cc race ahead of Frenchman Johann Zarco and Spaniard Maverick Vinales.
