After two days of roasting hot weather, dominated by Dani Pedrosa, rain arrived on Sunday, giving the underdogs a welcome chance to shine and increasing pressure at the front of the field - particularly when Pedrosa and second-on-the-grid Valentino Rossi were only 13th and 17th in the wet warm-up.
Meanwhile Stoner, who had struggled to a season's worst ninth in qualifying and needed to beat Rossi to wrap up the crown, had been an impressive second fastest in the warm-up - and charged up to third by the end of lap one.
Pedrosa defied his warm-up performance to snatch an early lead, and the Repsol Honda rider even made a slight break - before being reeled-in by wet weather specialist Anthony West. Unfortunately for the Kawasaki rookie, he had jumped the start and was given a ride-through penalty almost exactly as he passed Pedrosa for the lead on lap 2 of 24.
When West pulled into the pits a lap later, fellow Australian Stoner - having overtaken Pedrosa - inherited the advantage, but held it only briefly before being passed by Marco Melandri. The Gresini Honda rider had led the wet warm-up, charged quickly forwards from ninth on the grid and continued to lead until just after the halfway point.
Stoner had stuck to Melandri's rear wheel, but it was Rossi who eventually toppled his fellow Italian. The Doctor had dropped back to seventh on the opening lap, then made steady progress forwards and, as the track developed a clear dry line, was able to hunt down and pass title rival Stoner on lap 12.
Rossi's determination to take the lead almost saw him collide with Melandri, whom he had left hospitalised after a Motegi collision in 2005, but the #46 made a clean out-braking move stick at the end of on lap 14 - after which Melandri and Stoner immediately dived for the pits, with Rossi waiting one further lap.
The circuit was effectively dry by that stage and, with lower ranked riders gambling on a bike change much sooner, lap times proved that slick tyres were the way forward. Stoner, Melandri and Rossi were ultimately punished for staying out so long, since all three missed out on a podium, but few could blame them - Stoner and Rossi were concentrating on beating each other, while Melandri probably found it hard to surrender the grand prix lead.
When the order had sorted itself out, Capirossi had taken the lead - helped by a perfectly timed bike swap - with Kawasaki's Randy de Puniet, who had run off track while third in the early stages, in second place ahead of Melandri's team-mate Toni Elias and the Dunlop Yamaha Tech 3 of Sylvain Guintoli! Stoner and Melandri were fifth and sixth, but Rossi was down in 11th.
The Italian's problem wasn't the timing of his pit stop, since he rejoined in second behind Capirossi, but some form of issue with the front tyre of his second Fiat Yamaha, which prompted the former five times MotoGP world champion back into the pits to have his machine examined - all but handing Stoner the crown. Rossi was sent back out, but again struggled to slow his M1 - running wide at the end of the back straight - and he was left to limp home in a very unlucky 13th.