Stoner had blasted past pole sitter Chris Vermeulen to take an early lead into turn one - and was already 1.25secs ahead by the end of the opening lap - while Rossi made little impression, gaining only two places from his eleventh on the grid (set in Friday's rain)... and was still in ninth two laps later, four seconds behind Stoner.
But Rossi found his rhythm soon after, his special Fiat 500 liveried Yamaha carving past team-mate Colin Edwards and countrymen Loris Capirossi and Marco Melandri on lap four, then a fading Vermeulen one lap later.
The former five-times MotoGP champion then set about closing down fast-starting Repsol Honda team-mates Dani Pedrosa and Nicky Hayden; the #46 picking them off on successive laps to leave only John Hopkins between himself and Stoner.
Rossi vaporised a 2.6secs deficit to the Rizla Suzuki rider within three laps, then simply accelerated past the Anglo-American on the exit of a tight left hander. That impressive corner speed carried The Doctor to within half a second of five-times 2007 winner Stoner by the halfway stage of the 26 laps, but the ultra confident Australian far from rolled over.
For the next ten laps Rossi remained locked to the rear wheel of Stoner's Ducati, but once again the 21-year-old soaked up the pressure. After several trial runs into the final chicane, Rossi eventually launched his carefully planned attack at exactly that point at the end of lap 22 - then bolted for his third victory of the season.
The 28-year-old crossed the finish line 1.909secs clear of Casey and the relief was clear to see - the animated Italian literally shaking his M1 with delight as he took the chequered flag. Unsurprisingly, given the unpredictable nature of the season so far, there was no pre-planned celebration waiting for Rossi, although he did stop and sit on the bull's-eye of a giant Assen logo before returning to parc ferme.
Making a much slower return was Stoner, whose Ducati appeared to run out of petrol on the slow down lap - the first sign this season that any team may have been borderline on fuel. And Stoner wasn't alone; world champion Hayden also needed a push back to the pits after suffering what appeared to be the same problem.
But that minor inconvenience couldn't dampen Hayden spirits: The American, after finishing a best of just seventh from the opening eight races with the #1 plate, took his first podium of the year at Assen after an inspired ride that began with a brilliant 13th to sixth move into turn one.
The Kentuckian, finally riding and sliding his RC212V just as he likes, rose to third by lap four, lost the position to Rossi, then regained his first 800cc rostrum by passing countryman Hopkins on lap 14 of 26. Thereafter, Nicky held his own ahead of team-mate Pedrosa, and put four seconds on the Spaniard by the finish.