Webber beat out Red Bull teammate Sebastian Vettel for the prime starting position for Sunday's race, his first since last year's Korean Grand Prix.
Webber zoomed around the 3.6-mile Suzuka Circuit in 1 minute, 30.915 seconds -- 0.174 seconds faster than Vettel, who battled problems with his car's kinetic energy recovery system throughout the qualifying laps.
"We had a problem this morning, but I don't think that made a difference in terms of finding the rhythm," said Vettel, the F1 points leader. "We did have an issue in qualifying, but we are... Front row for the team, which is great."
Lewis Hamilton of Mercedes took the No. 3 starting position with a lap of 1:31.253. Romain Grosjean will start in the fourth position Sunday.