The reigning world champion, 26, announced yesterday he is to quit the sport at the end of the season, having denied he was planning to call time on his career at the previous round in Portugal.
In his announcement Stoner said he had lost his passion for bike racing as the championship moves towards production, as opposed to prototype, based rules.
But there was little evidence of any disillusionment today as the Repsol Honda rider topped both the day's sessions, with his afternoon lap of one minute 33.740 seconds putting him over a quarter-of-a-second clear of the rest of the field.
His team-mate Dani Pedrosa was his nearest challenger around the tight, twisting Bugatti configuration of the Le Mans circuit as the pair laid down an ominous marker to their rivals.
Yamaha's Jorge Lorenzo, who trails Stoner by a point at the top of the standings, was third fastest, but was almost 0.4 seconds adrift of Stoner's benchmark.
Alvaro Bautista made it three Hondas in the top four with a strong start to the weekend on the Gresini team's machine, edging out the second factory Yamaha of Ben Spies.
The Tech 3 Yamaha team were not quite able to match their impressive pace of the opening three rounds but were still looking competitive, with Andrea Dovizioso and Britain's Cal Crutchlow sixth and seventh fastest.
But Ducati's struggles continued. The custom Pramac bike of Hector Barbera beat the two factory machines to eighth spot, with Valentino Rossi and Nicky Hayden rounding out the top 10.
Randy de Puniet was once again the fastest of the CRT machines in 13th place on his Aspar Aprilia.
Crutchlow, who has made the best start to a MotoGP season by a British rider since 1988, admitted he was a little unhappy with the handling of his YZR-M1, but is confident his problems on corner entry can be solved in time for qualifying tomorrow [Saturday].
"We have a couple of small problems but nothing that I don't think we can fix ahead of the race," he said.
"I can't get the bike to turn into the corner as I'd like and I'm losing a little bit of time in that area. We will have a sit down tonight and see if we can come up with a set-up that will improve the turning.
"To be honest, Le Mans is not the best circuit for me and it is quite difficult. I've only been here once before and I crashed in the race last year, so a big part of my job today was just trying to gain some more experience with the layout.
"It was still a positive day and I am really close to Andrea and Ben, so with an improvement to the turning of the bike, I'm sure I can be even more competitive."