Despite qualifying fourth on the grid, behind three Michelin-shod Yamahas, Stoner was a firm pre-race favourite - but the young Australian had to work hard before he finally hit the front, on lap 8 of 22.
Repsol Honda's Dani Pedrosa got a lightening start from eighth on the grid to lead the 18-rider field into the first turn of the 2008 season, with rookie James Toseland and Tech 3 Yamaha team-mate Colin Edwards second and third, just ahead of rookie pole sitter Jorge Lorenzo of the factory team.
Valentino Rossi began his first grand prix with Bridgestone tyres by gaining two positions through the opening turns, placing the seven-times world champion between new team-mate Lorenzo and sixth-placed Stoner.
Stoner appeared to almost sit back and wait during the opening laps, while those ahead of him frantically fought for position, although a more technical theory was that he was saving fuel to be unleashed later.
By contrast, Lorenzo proved his nickname correct with a brave 'around-the-outside' pass on both Tech 3 riders at turn one, only to find combative fellow rookie Toseland shoving brutally back past him soon after.
Rossi then relegated Lorenzo a further position, before both Fiat Yamahas used their pneumatic-valve power to demote Toseland two places in one move along the 1 km main straight.
The Doctor was now free to hunt down Pedrosa, who had capitalised on the battles behind to build an early lead of 1.5secs - despite an injured hand - and the Spaniard was soon being reeled in by the charging Italian.
Rossi took the lead for the first time in 2008 on lap 5, but had dragged Lorenzo, Stoner and another fast rookie, Andrea Dovizioso, with him.
Pedrosa soon lost second place to countryman Lorenzo, then handed third to Stoner by running wide at turn one while trying to retaliate. It was now lap 7 and Stoner was firmly on the attack, the #1 slipping neatly past Lorenzo before, in a repeat of one year ago, rocketing by Rossi along the home straight - his Desmosedici now showing the kind of peerless top speed expected.