The Repsol Honda rider was the class of the field in practice and qualifying and backed up that pace today as he finished over eight seconds clear of team-mate Dani Pedrosa to register his eighth win in 14 races this season.
The Australian, whose first championship came with Ducati in 2007, now leads the riders' standings by 44 points from Yamaha's Jorge Lorenzo with four rounds remaining.
Stoner failed to make the most of his pole-position start off the line, out-dragged first by Pedrosa and then by Ben Spies as the Yamaha man took the lead into the first corner.
But Stoner was not be be denied, and overhauled both Pedrosa and Spies by the end of the opening tour en route to a victory by a commanding margin.
"We're pretty much back to our best," Stoner told BBC Sport.
"It felt good all weekend. The bike has been fantastic and the only problem was the wind - it was changing direction and speed every lap so that was a challenge but I just had to bring it home.
"It was my race to lose today and I did the job."
Pedrosa clung to his team-mate's coat-tails as best he could as he came in a distant second, but Spies could not maintain the pace and faded to an eventual fifth-placed finish.
Spies' demise allowed team-mate and reigning champion Lorenzo to come through for the final podium berth, the Spaniard finishing well clear of Italy's Marco Simoncelli (Gresini Honda), who ran third early on but dropped back after on off on lap 10.
Suzuki's Alvaro Bautista took a strong sixth place from Hector Barbera (Aspar Ducati) and Nicky Hayden (Ducati), while Britain's Cal Crutchlow took ninth for Tech 3 Yamaha, ahead of Valentino Rossi, who continued his struggles on the factory Ducati.
The race saw a number of riders crash out in the windy conditions, the most notable coming when Honda's Andrea Dovizioso, currently lying third in the riders' standings, lost control on the first lap to register his first retirement of the campaign.