Stoner was fastest in the morning session and he stayed at the top in the afternoon, the Repsol Honda rider took over the top spot from his teammate Dani Pedrosa with eight minutes left in the 45-minute session.
Stoner then improved a bit more and ended up with a best of 1:33.740 - .265 of a second clear of Pedrosa, the Spaniard back at the track where he suffered a broken collarbone last year.
Yamaha's Jorge Lorenzo improved from sixth in the morning session to third in the afternoon, the Spaniard coming into the French Grand Prix a point behind Stoner in the fight for the championship. He ended up .396 of a second behind his Australian rival.
Fourth place was a surprise with Gresini Honda's Alvaro Bautista putting in his best effort of the season to best Ben Spies and the factory Yamaha. Spies suffered a crash at one point in the afternoon session. Sixth and seventh went to Monster Energy Tech 3 Yamaha's Andrea Dovizioso and Cal Crutchlow, respectively.
The top Ducati rider ended up being Pramac's Hector Barbera with Marlboro Ducati's Valentino Rossi and Nicky Hayden rounding out the top 10.
The top CRT bike was Randy de Puniet's Aspar mount, the Frenchman ending up 13th. Chris Vemeulen, filling in for the injured Colin Edwards, ended up last in his return to MotoGP racing.
1. Casey Stoner (Honda) 1:33.740
2. Dani Pedrosa (Honda) 1:34.005
3. Jorge Lorenzo (Yamaha) 1:34.136
4. Alvaro Bautista (Honda) 1:34.437
5. Ben Spies (Yamaha) 1:34.467
6. Andrea Dovizioso (Yamaha) 1:34.585
7. Cal Crutchlow (Yamaha) 1:34.610
8. Hector Barbera (Ducati) 1:35.079
9. Valentino Rossi (Ducati) 1:35.112
10. Nicky Hayden (Ducati) 1:35.132