Casey Stoner will start his final Phillip Island MotoGP race from pole position, despite a highside in qualifying.

The Australian, unbeaten on home asphalt since 2007, has dominated his penultimate grand prix event before retirement, but things didn't go completely to plan in qualifying.

Stoner, who returned from ankle surgery two races ago, was thrown off his factory Honda at the 20-minute mark of the hour, after swapping a softer rear tyre for the harder spec.

But he soon returned on his spare machine, then repeatedly improved his pole time to conclude the session 0.517s ahead of Yamaha's title leader Jorge Lorenzo.

Stoner's Repsol Honda team-mate Dani Pedrosa was the only other rider within one-second of pole.

"To be honest it's been really nice to be back - and not just back at this circuit but feeling a little bit more comfortable," said Stoner, who hasn't won since before his Indianapolis ankle injuries.

"Most of the critical corners are on the left, so I'm actually able to relax on the right-hand turns, because they are not so critical, and put more effort in on the left.

"And it's been nice to ride one of these bikes around this track again. You know, it could well be my last [time]. I'm trying to enjoy every minute of it really. We've been having a fantastic weekend so far, just getting faster and faster."

Stoner wasn't sure what had caused the accident, but felt it was related to engine-braking rather than a cold tyre.

"I was on my out-lap with a hard tyre and the thing just decided to flick me," he said.

"Something locked up to do with engine-braking. I don't know if we were going too slow into the hairpin or what. But it completely came around on me and there was no way to stop it.

"So I was very fortunate not to come down on my foot. If it was the other way it would have been a different story.

"And then we were able to improve the lap time and still get pole.

"Big thanks to the team. It was a hectic session and things didn't really go to plan but the rest of the weekend has.

"So just happy to be on pole for the home grand prix and hopefully have something to celebrate tomorrow for everybody."