Casey Stoner was quickest in the Phillip Island warm-up by a crushing margin of nearly two seconds.
In mostly dry conditions, Stoner found far more grip than anyone else and was already over a second clear before his final lap of 1m30.942s put him 1.89sec ahead of nearest rival Marco Simoncelli (Gresini Honda).
Ducati rider Stoner will start on pole at home for a third consecutive year, and is chasing a fourth straight victory in Australia.
Stoner aside, Gresini was at the forefront throughout the 20-minute session, with Marco Melandri looking set to join Simoncelli among the leaders had he not spent much of the final minutes trying to extract himself from the marsh-like conditions of the run-off at the first corner.
Nicky Hayden managed to get back off the wet grass without too much difficulty when he went off on his Ducati, but Ben Spies had a gentle fall when his Tech 3 Yamaha slid off at the hairpin and lost grip in the gravel.
Valentino Rossi was third for Yamaha, while his world champion team-mate Jorge Lorenzo did not make a serious effort at a lap time and was the last of the 15 riders – both Dani Pedrosa and Loris Capirossi having now pulled out of the race due to injuries.
Pos Rider Team Time Gap
1. Casey Stoner Ducati 1m30.942s
2. Marco Simoncelli Gresini Honda 1m32.832s + 1.890s
3. Valentino Rossi Yamaha 1m32.913s + 1.971s
4. Andrea Dovizioso Honda 1m33.023s + 2.081s
5. Colin Edwards Tech 3 Yamaha 1m33.106s + 2.164s
6. Randy de Puniet LCR Honda 1m33.266s + 2.324s
7. Marco Melandri Gresini Honda 1m33.393s + 2.451s
8. Hiroshi Aoyama Interwetten Honda 1m33.599s + 2.657s
9. Nicky Hayden Ducati 1m33.636s + 2.694s
10. Mika Kallio Pramac Ducati 1m33.709s + 2.767s
11. Aleix Espargaro Pramac Ducati 1m34.834s + 3.892s
12. Hector Barbera Aspar Ducati 1m34.874s + 3.932s
13. Alvaro Bautista Suzuki 1m35.191s + 4.249s
14. Ben Spies Tech 3 Yamaha 1m35.306s + 4.364s
15. Jorge Lorenzo Yamaha 1m52.957s + 22.015s