The threat of rain added extra tension to the one hour session, the first half of which saw Pedrosa take charge on race tyres.
When qualifying rubber appeared, last year's wet race winner
Chris Vermeulen briefly took the advantage, before being replaced at the top by Pedrosa and then
Valentino Rossi.
But
Colin Edwards, fastest in morning practice and second to Pedrosa on race rubber earlier in qualifying, then delivered a superb lap to pull a huge 0.7secs ahead of Rossi at the front of the field - and lowered pole yet again with ten minutes to go.
Rossi, Pedrosa and world champion
Casey Stoner then began steadily chipping away at the Texan's advantage, but the Tech 3 Yamaha star was still 0.220secs clear of Ducati star Stoner with two minutes to go, but which time Casey had finished his qualifying attack.
The only man capable of depriving Tech 3 of an emotional home pole was now Pedrosa and the world championship leader saved his best for last - snatching his and Honda's first pole of the season by 0.127secs.
Edwards, on pole last time out at Shanghai, was denied a last gasp defence when he caught a slow moving
Marco Melandri at the wrong place - and made his feelings to the Ducati rider known - but still secured a Michelin one-two for the French manufacturer's home event.
Stoner, still losing time in the twisty final sector, was more than happy with a front row start - but believed he had the speed for pole - while Rossi was a little disappointed to have been left 0.5secs from the top and facing a second row start.
Rossi's Fiat Yamaha team-mate
Jorge Lorenzo took the first three pole positions of the year, but the injured rookie, riding with two fractured ankles after his Shanghai accident, had suffered his second fall of the weekend during Saturday morning practice.
The Spaniard head butted the ground and was sent tumbling through the gravel after losing the front of his M1 - then shot straight on at turn one this afternoon, just managing to stay in control of his bouncing machine.
