With Le Mans typically experiencing four seasons in a day morning rain gave way to afternoon sunshine, with provisional pole changing hands several times, before Pedrosa made it his own with a best effort of 1í33.974 on his final lap, to take first spot by a 0.005s margin.
The factory Honda rider who appears to be getting stronger every time he gets on his RC212V at present, following an injury plagued winter, will be joined on the front row by fellow Spanish rider Jorge Lorenzo (Fiat Yamaha) and Casey Stoner (Ducati Marlboro).
Valentino Rossi made improvements as the session went on, his final position of fourth being a significant step forward having lapped eleventh fastest on Saturday morning.
Rossiís compatriot Andrea Dovizioso (Repsol Honda) and his former team-mate Colin Edwards, who briefly held provisional pole in the session, will line up behind him on the grid.
The third row will feature Rizla Suzuki pair Chris Vermeulen and Loris Capirossi who both qualified within a second of Pedrosa, at a track where Vermeulen took victory in 2007.
The top ten was rounded off by Italian competitor Marco Melandri (Hayate Racing) and home rider Randy de Puniet (LCR Honda) who both bounced back from crashes in the hour-long session.
The weathermen have suggested that there is an 80% chance of rain on Sunday at the time of the fourth MotoGP race of the year.