The reigning world champion secured his place at the top of the timesheet with his 54th and final lap of the opening day.
Breaking the 1:40 barrier with five of his laps, it was the Repsol Honda rider's final turn of the session which left him 0.273s quicker than Jorge Lorenzo.
Stoner's blistering lap of 1:39.146 came after the Australian spent most of the latter part of the day heading out for runs of between three and four laps, as many riders found increasingly windier conditions harder to deal with.
Yamaha Factory Racing rider Lorenzo had occupied top slot for the majority of the day, as he focused on the electronics settings on his YZR-M1 to aid an improvement in acceleration.
Lorenzo’s best time of 1:39.419 was set on the 46th of a tiring 76 laps, and at one point the Spaniard set five sub-1:40 laps on the trot as he rode with a similar set-up to the one used at the last Test at Sepang.
Dani Pedrosa got under 1:40 once and it was that lap of 1:39.579 which left the Repsol Honda rider third on the timesheet at the conclusion of the day.
The Spaniard highlighted an improvement in braking as the main outstanding issue to be tackled on the RC213V.
In fourth position Ben Spies, who at one stage had led the timings with his best lap of 1:39.984, ended 0.838s off Stoner with his top effort.
Monster Yamaha Tech 3's Cal Crutchlow was the fastest non-factory rider in 1:40.130, with Nicky Hayden the quickest Ducati in sixth.
Alvaro Bautista was unharmed following a crash early in the day as he continued his adaptation to the RC213V with the seventh-best time, and Andrea Dovizioso tried to concentrate on the base setting of his M1.
In ninth spot, Valentino Rossi struggled to a best time of 1:40.920, almost 1.8s off Stoner. The nine-times World Champion explained at the end of the day that he was losing time on corner entry.
1 Casey STONER (Repsol Honda Team) 1:39.146
2 Jorge LORENZO (Yamaha Factory Racing) 1:39.419
3 Dani PEDROSA (Repsol Honda Team) 1:39.579
4 Ben SPIES (Yamaha Factory Racing) 1:39.984
5 Cal CRUTCHLOW (Monster Yamaha Tech 3) 1:40.130
6 Nicky HAYDEN (Ducati Team) 1:40.512
7 Alvaro BAUTISTA (San Carlo Honda Gresini) 1:40.545
8 Andrea DOVIZIOSO (Monster Yamaha Tech 3) 1:40.665
9 Valentino ROSSI (Ducati Team) 1:40.920
10 Stefan BRADL (LCR Honda) 1:40.983