Ducati Marlboro's amazing young star had fluffed his start and plummeted from fifth on the grid into turn one, while pole sitter Colin Edwards took an early lead. However, it was 2006 event winner Dani Pedrosa who underlined his growing wet weather credentials by leading the field across the line at the end of lap one.
The young Spaniard continued to reign until lap five of 30, when Edwards regained control - but an amazing surge from Stoner meant the Australian was already up to third and, after passing a rapidly fading Pedrosa, was soon locked onto Edwards' rear wheel.
Edwards proved a tough opponent for Stoner, who remained just a few tenths behind the Texan for lap after lap as the pair pulled away from the field - but the pivotal moment came just after the halfway stage.
Edwards' Michelins and Stoner's Bridgestones had looked evenly matched during the early part of the grand prix, but with a dry line starting to appear the Japanese rubber had an ever-increasing edge. All it took was a slight bobble by Edwards into the Melbourne Hairpin on lap 16 for Stoner to strike; the 21-year-old then punching out several flat-out laps to break the former double World Superbike champion.
Stoner went on to win by almost 12 seconds, while Edwards took his second podium of the season with a safe runner-up finish. Nevertheless, MotoGP's pole position jinx continues, while Edwards remains winless after 74 starts.
Completing the podium was wet weather star Chris Vermeulen, winner in the rain at Le Mans, who rose quickly from 12th on the grid to fourth - indicating he would be a victory contender - but then suffered a mid-race loss of form, costing him positions to Valentino Rossi and Rizla Suzuki team-mate John Hopkins.
Rossi had made a relatively poor start from second on the grid, leaving him fifth at the first turn. Despite some tough battles, and a mistake at Coppice, the Italian then muscled his way up to third - albeit eight seconds behind Edwards and Stoner - by the midway point.
But the #46 was unable to reel in the top two and, with the track drying, found himself increasingly under pressure from a resurgent Vermeulen - who bridged a four-second gap within six laps, then easily outbroke Rossi at the end of the back straight with four laps to go. Vermeulen ran out of time to catch Edwards, but undoubtedly had the pace.
Rossi's subdued fourth place dealt yet another blow to his championship aspirations and the former five-times MotoGP champion has now dropped 26 points, over one race win, behind Stoner - who has now won in the wet, the dry, by coming from behind and by leading from the front. Coupled with Ducati's impressive Desmosedici motorcycle and Bridgestone's enduring tyres, Stoner simply has no weaknesses at present.