Stoner went clear early on and rarely looked troubled thereafter, and for half the session was almost one second clear of the field.
When others, chiefly his Honda stable-mate Dani Pedrosa, did close in, the Australian went back out and lowered his benchmark further, ending the session 0.587 seconds clear of Pedrosa.
There was a flurry of improvements as the flag fell. Tech 3 Yamaha's Andrea Dovizioso claimed third, while his team-mate Cal Crutchlow simultaneously moved into seventh.
Little more than a quarter of a second separated the pair, but that gap was still enough for three other riders: the two works Yamahas of Ben Spies and Jorge Lorenzo, fourth and sixth respectively, and the Pramac Ducati of Hector Barbera.
Gresini's Alvaro Bautista finished eighth ahead of the two works Ducatis, both of which had run within the top six for much of the session before being bumped down by the late improvements.
Valentino Rossi, who scored his last MotoGP podium at the French circuit last year, finished more than 1.5s down on Stoner but did complete the most laps of any rider.
Aspar's Randy de Puniet was once again the fastest CRT rider in 13th, while Chris Vermeulen - replacing the man de Puniet hit at Estoril, Colin Edwards - made an understandably cautious start, finishing last and outside the 107 per cent marker.