Casey Stoner will start from pole position for his home grand prix at Phillip Island for the second year in a row.
The Australian Ducati rider was dominant for most of the hour, and fended off a strong late challenge from Yamaha's Valentino Rossi. The result is only Stoner's second pole position of his illness-marred season.
While Rossi failed to get pole, he will be comforted by his title rival and teammate Jorge Lorenzo's continued struggles. Lorenzo only qualified fourth, a scant 0.001sec behind Honda's Dani Pedrosa.
Stoner was fastest throughout the race practice part of the session, extending his advantage to half a second before the flying laps started at the end and Rossi managed to close in. Rossi deposed the local hero with six minutes to go, edging ahead by just 0.075sec. But Stoner soon responded, squeezing back in front by a tiny 0.005s two minutes from the end.
Both stayed out hoping to squeeze some more speed from their existing tires, and while Rossi failed to gain any time, Stoner managed to extend his pole margin to a slightly more comfortable 0.050sec.
Pedrosa recovered from a mid-session crash to take third. The Honda slid to the ground at high-speed going into the Southern Loop as drizzle briefly fell. Despite tumbling across the grass, Pedrosa quickly got up unhurt and returned to the pits for his spare bike.
Lorenzo failed to qualify on the front row for the first time all year, but having languished further down the top ten for much of the hour, fourth still counted as damage limitation.
Gresini Honda's Alex de Angelis also crashed during the session, falling at MG corner early on. But he too recovered rapidly and built on his promising practice form by qualifying sixth behind Colin Edwards (Tech 3 Yamaha).
Nicky Hayden put the second factory Ducati seventh, ahead of LCR Honda's Randy de Puniet, Pramac Ducati's Mika Kallio, and Andrea Dovizioso on the second works Honda.
MotoGP's other Australian rider Chris Vermeulen (Suzuki) had a terrible session in his last home appearance before heading back to Superbikes. He struggled for speed all afternoon and will start on the penultimate row, ahead of only Scot Honda's Gabor Talmacsi.
Only 16 bikes will take the start tomorrow, with Pramac Ducati's Niccolo Canepa sidelined by the arm injuries he suffered in his practice crash.
Pos Rider Bike Time Gap
1. Casey Stoner Ducati 1m30.341s
2. Valentino Rossi Yamaha 1m30.391s + 0.050s
3. Dani Pedrosa Honda 1m31.070s + 0.729s
4. Jorge Lorenzo Yamaha 1m31.071s + 0.730s
5. Colin Edwards Tech 3 Yamaha 1m31.096s + 0.755s
6. Alex de Angelis Gresini Honda 1m31.260s + 0.919s
7. Nicky Hayden Ducati 1m31.325s + 0.984s
8. Randy de Puniet LCR Honda 1m31.380s + 1.039s
9. Mika Kallio Pramac Ducati 1m31.384s + 1.043s
10. Andrea Dovizioso Honda 1m31.472s + 1.131s
11. Toni Elias Gresini Honda 1m31.640s + 1.299s
12. James Toseland Tech 3 Yamaha 1m31.722s + 1.381s
13. Loris Capirossi Suzuki 1m31.873s + 1.532s
14. Marco Melandri Hayate Kawasaki 1m32.190s + 1.849s
15. Chris Vermeulen Suzuki 1m32.338s + 1.997s
16. Gabor Talmacsi Scot Honda 1m32.752s + 2.411s