The 2007 World Champion is gearing up for his first season on the Repsol Honda and has been untouchable all winter.
The Australian was again fastest as he lapped the Malaysian track in a best time of two minutes 0.987 seconds, with team-mate Dani Pedrosa in second and reigning champion Jorge Lorenzo third on the Fiat Yamaha.
Stoner said: "We had a really good day and from the beginning I felt more comfortable with the bike again, like I understood the bike a little better.
"We're very happy with the progress we made and everything and everybody seems to be working well".
Lorenzo said: "With the improvements we've made we can now brake a little later and enter the corners a little more quickly as well so I was able to do some good fast consistent lap times this afternoon when it was still very hot on the track."
Valentino Rossi was down in ninth as he continues to adapt to his move to Ducati while returning to fitness from a shoulder operation and British hope Cal Crutchlow struggled as he crashed twice while battling with food poisoning.