The Repsol Honda rider opted to head out onto the famous grid with a soft rear tyre - a risky choice that paid off, with the Aussie finding pace from the outset to fight out the front with Yamaha Factory Racing rival Jorge Lorenzo.
Stoner made his move with eleven laps remaining, stealing the lead from Lorenzo and holding firm until the chequered flag to bring home the race with a winning margin of 3.429 seconds. The World Champion's teammate Dani Pedrosa filled out the Laguna Seca rostrum, clinching third after coming home 7.633 off pace.
The race win sees Stoner hold onto the third rung of the Championship ladder with 173 points, biting at the heels of Pedrosa on 182 and Lorenzo on 205 going into Round 11 at Indianapolis next month.
The victory marks Stoner's fourth for the season, and his 37th premier class win - bringing him level with Mike Hailwood in 4th in overall premier class victories behind Rossi (79), Agostini (68) and Doohan (54).
After two disappointing outings in Mugello and Sachsenring, and a difficult weekend at Leguna Seca trying to make the hard tyre work on his machine, Stoner was pleased with the result.
"It's been a difficult weekend for us in general especially trying to make the hard tyre work. So for the race I decided to go with the soft option and be a little more careful with the tyre, keep a little more traction and not spin so much," Stoner reflected after the race.
"At the beginning of the race I tried to move to the front but Dani and Jorge were riding very good lines and it was impossible to get past. I decided to slow the lap times a little and try to save the tyres until the end and then we could start to come back.
"I was confident for the entire race that I had enough pace for the win, we just needed to make sure the tyre would last until the end. When we go the front we put in some good laps and pulled some small advantage and just continuted from there. I'm very, very happy and a big thanks to all the team."
The 2012 MotoGP World Championship now heads into summer break, before bursting back into action at Indianapolis from 17-19 August.
For all the latest news, information and results head to www.motogp.com.