The Spaniard, yet to start lower than second in 2012, rose to the top almost immediately after the session began, and soon dropped down to a 1m37.710s.
Fifteen minutes into the session he lost the front at Turn 8, sliding into the gravel, but was able to rejoin with help from marshals and returned to the pits for repairs.
With Marquez in the pits the session seemed to be building to a final shoot-out, especially when Paddock Suter's Thomas Luthi - the only other rider to have been on pole this year - got to within 0.029 seconds of Marquez.
Any prospect of a final flurry was spoiled however as rain fell with five minutes of the session remaining, effectively freezing the order and handing Marquez his third pole in the opening four races.
"It was so difficult - we knew at the end of practice it might start raining so we tried to push in the beginning," Marquez said. "When I crashed I braked too late, tried to go in anyway but it was too hard. I have a good feeling after going out again, and lapping well, so I think I can do a good race."
Luthi ended second, ahead of Marquez's nearest championship challenger Pol Espargaro (Pons Kalex) and Scott Redding (Marc VDS Kalex), the latter of whom also fell in the final minute.
Redding's stable-mate Mika Kallio was another to have a moment as conditions around the French circuit remained tricky, but he did enough to end sixth fastest behind Andrea Iannone (Speed Master).
Forward Suter's Alex de Angelis claimed seventh ahead of Johann Zarco (JIR Motobi) and Claudio Corti (Italtrans Kalex), with the latter pair finishing just over one second down on Marquez's best.
Toni Elias (Aspar Suter), a Moto2 racewinner at Le Mans in 2010, rounded out the top 10.