After leading all three practice sessions, despite a fall on Saturday morning, Casey Stoner was the overwhelming favorite to claim pole at Le Mans.
But a heavy rain shower between final practice and qualifying saw the track drying throughout the one-hour grid-deciding afternoon session.
Reigning world champion and 2012 leader Stoner, who announced he will retire from MotoGP on Thursday, put his Repsol Honda at the head of the timesheets five times during the hour.
But the Australian was forced to abandon his final run, leaving him second on the grid to team-mate Dani Pedrosa by 0.303s.
"We're really happy to be on front row, but qualifying definitely didn't go to plan,” said Stoner, last year's Le Mans winner. “The track was drying out and we knew we had the pace, you just had to be a little cautious in some areas that were still holding water.
“We felt we were fast enough to be on pole position but every time I was on a good lap or building up to one, I got held up. I tried to drop back and give myself some space but I still managed to catch up to a CRT bike in front of me which ruined that lap.
“Then the next lap we were doing pretty well but I saw yellow flags and rain so I backed off, unfortunately the rain wasn't heavy enough to upset my lap and I could have continued it, but that's the way it goes sometimes.
“I think we're looking good for the race, we're pretty comfortable in dry conditions but we still have warm up and a chance for the others to find something extra, so we're going to have to improve our bike a little also and wait for the race as the weather conditions are still unpredictable".
Stoner will start Sunday's fourth round with a single point advantage over Yamaha's Jorge Lorenzo, who qualified fourth.