Stoner rejoined in a safe second position, while Rossi made a double-take at his pit board when it revealed his now untouchable lead the next lap around.
Rossi officially won his fourth race of the season, and first since Mugello on June 1, by 13.001secs from Stoner, and celebrated by kissing the asphalt at the top of the corkscrew. Rossi's previous best finish at Laguna Seca was third in 2005.
Rossi now leads the 2008 world championship by an enlarged 25 points from Stoner heading into the summer break, with the absent Dani Pedrosa
dropping to third.
Stoner, who later criticised some of Rossi's moves, brought his Ducati home 13.608secs in front of third placed Chris Vermeulen.
Vermeulen had indicated his podium potential during free practice, but qualified just eighth on the grid. The Rizla Suzuki rider, third last Sunday in the German rain and something of a Laguna Seca specialist, was up to fifth by the end of the opening lap and eventually levered third place from home hero Nicky Hayden
and JiR Honda rider Andrea Dovizioso.
Dovizioso did his hopes of securing Hayden's factory ride for 2009 no harm by taking fourth place from the Repsol Honda rider with eleven laps to go, then holding off the double US GP winner by less than one second at the line - making Dovi the highest placed Michelin rider.
Most Michelin riders had struggled badly with over-conservative tyres during practice, but some faired better than they had feared in the race - despite an all-Bridgestone podium - with Honda LCR's Randy de Puniet
completing a Michelin fourth, fifth and sixth in the main event.
Alice's Toni Elias
finished as the second best Ducati rider in seventh, but was capable of much more had he not dropped from sixth to tenth on lap six... and then back to twelfth place on lap eight.
Reigning double AMA Superbike champion Ben Spies finished his second MotoGP race in eighth position for Rizla Suzuki, a result he didn't seem too impressed with. James Toseland
was also unhappy after slipping from fifth on the grid to ninth for Tech 3 Yamaha, while Shinya Nakano
completed the top ten for Gresini Honda.
Kawasaki's replacement rider Jamie Hacking matched AMA rival Spies for much of the race before losing out to Elias and Nakano in the closing stages, costing him his target of a top ten finish by just one position.