The first ten laps of the Australian Grand Prix saw Stoner put under a surprising amount of pressure by outgoing world champion Nicky Hayden, before the American's rear tyre began sliding a little too much.
The Repsol Honda rider soon lost second to Valentino Rossi as a result, but far worse was to follow when an engine failure forced a furious Hayden to park his RC212V just before the midway point of the 27 laps.
Meanwhile, Rossi was unable to remotely match Stoner's searing pace and the 21-year-old had already pulled 4.6secs clear of the Fiat Yamaha star by the end of lap 14.
Stoner's advantage then increased to 6.7secs over an Italian at the chequered - but it wasn't Rossi...
During the closing stages of the race Stoner's team-mate Loris Capirossi put on a spirited charge, finally passing fading fellow Italian Marco Melandri for fourth on lap 18, then overtaking both
Rossi and pole sitter Dani Pedrosa in a single move two laps later. The Motegi race winner went on to put over three seconds between himself and lead Michelin rider Rossi by the finish, with Pedrosa a further 1.6secs back.
By then, Stoner was already celebrating his ninth win of the season - and first ever home victory - by carrying a huge Australian flag before being cheered on the podium by a start-finish straight packed with delighted fans.
Ducati had particular reason to celebrate, having secured the 2007 teams' and manufacturers' world titles to add to Stoner's riders' championship. The Italian marque is the first European manufacturer to win the constructors' crown since MV Agusta in 1973.
Behind the top four, Pramac d'Antin's Alex Barros finished comfortably ahead of Kawasaki's Randy de Puniet for fifth position, while John Hopkins salvaged seventh from a nightmare weekend for Rizla Suzuki. Team-mate Chris Vermeulen also improved substantially on his qualifying position to finish one place, but 5.6secs, behind the Anglo-American with Rossi's team-mate Colin Edwards and Melandri completing the top ten.
Melandri had looked like a podium finisher earlier in the race, but lost a huge amount of time in the closing stages due to a suspected tyre problem.
New d'Antin Ducati rider Chaz Davies, competing in his second MotoGP race, retired just before the halfway stage with some form of technical trouble. The 20-year-old, who had qualified 17th, reached a high of 14th prior to his problems.
The Malaysian Grand Prix will take place next weekend at Sepang, with the season ending Valencian Grand Prix on November 4.
Australian Grand Prix:
6. de Puniet