Drying conditions as the hour-long session unfolded allowed the Spaniard to clock one minute 33.638 seconds and take his first pole of the season and the fourth of his career at the French circuit.
Stoner was second-fastest with Andrea Dovizioso third, his best grid position this season, for Monster Yamaha Tech 3.
The Italian led the timesheets with five minutes remaining but Stoner ducked narrowly under his time, only for Pedrosa to power to pole in the closing stages.
The second row sees Yamaha Factory pair Jorge Lorenzo and Ben Spies sandwiching Dovizioso's fifth-placed team-mate Cal Crutchlow, who set the early pace in the wet but was unable to step up later in the session.
Valentino Rossi is seventh for Ducati ahead of Alvaro Bautista, who crashed out of a late flying lap on his San Carlo Honda Gresini. Karel Abraham completes row three.
Home favourite Randy de Puniet was 12th but his Power Electronics Aspar colleague Aleix Espargero was forced back to the pits by a mechanical problem.
The changing conditions accounted for LCR Honda's Stefan Bradl as he switched too early to slick tyres and crashed out.