Set in the afternoon session, Stoner's time in the high 1.29s was over eight tenths ahead of his Repsol Honda teammate Dani Pedrosa, who was nonetheless improving steadily across the session, with his sole aim this weekend to finish ahead of Jorge Lorenzo.
Stoner is not showing any signs of his injury, as he looks in breath-taking form ahead of his quest to take his sixth consecutive win at the track.
It was Yamaha Factory Racing's Lorenzo, who could clinch the world title on Sunday, that occupied third spot on the timesheets, albeit over a second off the top time set by Stoner.
Monster Yamaha Tech 3's Cal Crutchlow came in fourth, with the Brit doing extremely well to overcome flu type symptoms he has been experiencing since leaving Malaysia earlier this week.
In fifth, his teammate Andrea Dovizioso had a solid day, though will have to find something extra if he is to take third spot in the championship off Stoner this weekend.
Behind him in sixth, San Carlo Honda Gresini's Álvaro Bautista was on good form, seemingly finding some of the confidence in the bike he had two weeks ago in Motegi.
Seventh place went to his satellite counterpart Stefan Bradl on his LCR Honda MotoGP machine, who was the last of the riders to be within two seconds of the top.
Ducati's Valentino Rossi ended the day in eighth as top Desmosedici, although the Italian, who has won at this track five times in his career, will no doubt be looking for a lot more.
In ninth, his teammate Nicky Hayden was the only rider in the top ten to not better his time in the afternoon practice session.
Power Electronics Aspar's Randy de Puniet completed the top ten, with the Frenchman not only finishing as top CRT, but also beating the satellite Ducatis of Pramac Racing Team's Héctor Barberá and Cardion AB Racing's Karel Abraham.
The only crasher was San Carlo's Michele Pirro in the morning session, who initially produced an incredibly save from a big highside - only then to fall once he ran into the dirt.
He was able to re-join the morning session for the final part. Yamaha's Ben Spies is absent for the rest of the season as he recovers from surgery on his injured shoulder.