Stoner came off in the first session at Phillip Island but recovered to top the timesheets and was similarly dominant in the second spell over the course of the 45 minutes.
The Australian Repsol Honda rider needs to outscore nearest rival Jorge Lorenzo by 10 points on Sunday to take the title in a race he has won four times in a row.
Stoner produced a best lap of one minute 30.535 seconds - a tenth slower than he achieved on Friday morning - to see off reigning champion Lorenzo, who had earlier led with 1m 31.111sec.
Marco Simoncelli then came up with 1m 30.912sec to leap above the Spaniard before Stoner took control.
Factory Yamaha man Lorenzo ultimately ended up third ahead of team-mate Ben Spies with Dani Pedrosa (Repsol Honda) in fifth.
Despite topping the times, Stoner admitted he was far from happy with the set-up of his bike heading into the rest of the weekend.
"I don't feel totally comfortable with the bike and I'm sure we can improve the bike a lot," he said.
"The track is certainly a lot more bumpy than last year and I think it will be very difficult to get the bike feeling 100% as the circuit is making things worse.
"In general we've found the Honda is better in certain aspects than what we had last year but with these bumps it's difficult to compare in other areas.
"We need to get the bike riding the bumps in the front a lot better, and also find some more rear grip.
"There is still a lot of work before we find the right race set up and we know we can go a lot faster."