Casey Stoner had an off-track moment, while Valentino Rossi, Karel Abraham and Kris McLaren all walked away from falls during the session. McLaren was again outside of the 107% time.
Yamaha's Ben Spies will miss the remainder of the season after undergoing surgery to repair shoulder injuries at the Malaysian Grand Prix.
Local rider Kris McLaren has been drafted into the Avintia Blusens squad in place of the injured Yonny Hernandez this weekend.
CLICK HERE for pictures from the grand prix...
1.
Casey Stoner AUS Repsol Honda (RC213V)
1m 29.888s 2.
Jorge Lorenzo ESP Yamaha Factory Racing (YZR-M1)
1m 30.335s 3.
Dani Pedrosa ESP Repsol Honda (RC213V)
1m 30.629s 4.
Cal Crutchlow GBR Monster Yamaha Tech 3 (YZR-M1)
1m 31.195s 5.
Andrea Dovizioso ITA Monster Yamaha Tech 3 (YZR-M1)
1m 31.339s 6.
Stefan Bradl GER LCR Honda
MotoGP (RC213V)
1m 31.406s 7.
Alvaro Bautista ESP San Carlo Honda Gresini (RC213V)
1m 31.861s 8.
Karel Abraham CZE Cardion AB Motoracing (GP12)
1m 31.896s 9.
Nicky Hayden USA Ducati Team (GP12)
1m 31.954s 10.
Randy De Puniet FRA Power Electronics Aspar (ART CRT)
1m 31.984s 11.
Aleix Espargaro ESP Power Electronics Aspar (ART CRT)
1m 32.228s 12.
Valentino Rossi ITA Ducati Team (GP12)
1m 32.287s 13.
Hector Barbera ESP Pramac Racing (GP12)
1m 32.372s 14.
Michele Pirro ITA San Carlo Honda Gresini (FTR-Honda CRT)
1m 33.864s 15.
James Ellison GBR Paul Bird Motorsport (ART CRT)
1m 33.922s 16.
Danilo Petrucci ITA Came IodaRacing (Suter-BMW CRT)
1m 33.959s 17.
Ivan Silva ESP Avintia Blusens (FTR-Kawasaki CRT)
1m 34.209s 18.
Roberto Rolfo ITA Speed Master (ART CRT)
1m 34.394s 19.
Colin Edwards USA NGM Forward Racing (Suter-BMW CRT)
1m 34.520s 20.
Kris McLaren AUS Avintia Blusens (FTR-Kawasaki CRT)
1m 36.701s Pole position:Casey Stoner AUS Honda
1m 29.623sOfficial Phillip Island MotoGP records:Best lap: Casey Stoner AUS Ducati
1m 28.665s (2008)
Fastest race lap:Nicky Hayden USA Honda
1m 30.059s (2008)