Nicky Hayden ran second to Stoner in the early stages, before being shuffled back to sixth by lap ten. The Ducati rider was still in that position when the rain arrived, when he made an ill-fate gamble to pit for his wet weather bike, which cost him a position to fellow American Colin Edwards (Monster Yamaha Tech 3).
Hayden would have lost two places - Pramac Ducati's Randy de Puniet also moved ahead when he pitted - had Suzuki's Alvaro Bautista not crashed.
The withdraw of Lorenzo put Bautista - already due to make a MotoGP best start of fourth on the grid - into a front row place. The Spaniard held fifth on lap one, was demoted by Pedrosa, then regained fifth by passing a fading Hayden on lap 10.
Hayden's factory Ducati team-mate Valentino Rossi then became a bigger threat, but the Italian crashed out when he attempted an inside pass on Bautista into the off-camber MG hairpin on lap 14.
Bautista thus looked set for a safe fifth until he was caught out by the rain. Hiroshi Aoyama (Gresini) and Cal Crutchlow (Tech 3) - who had been eighth and ninth - fell on the same lap.
All of which meant that LCR's Toni Elias, Pramac's Loris Capirossi, returning to action after another shoulder dislocation, and Karel Abraham (Cardion AB) were the final finishers in eighth, ninth and tenth. Elias and Capirossi were one lap down, with Abraham - who fell - two laps behind.
Only 14 riders began the race, with Australian Damian Cudlin, due to make his second MotoGP appearance in as many events - this time for Aspar Ducati - joining the Yamahas riders on the sidelines due to injuries from a huge Saturday morning highside.
The penultimate round of the season, the Malaysian Grand Prix at Sepang, takes place next weekend.
Australian Grand Prix:
6. de Puniet