The Australian had trailed Ben Spies on the American's home soil after free practice in the morning but, after lamenting the lack of grip on the newly resurfaced track, he came on strong to impress in the late session.
Yamaha Factor Racing's Spies had done well with a best time of one minute 40.918 to shave two seconds off his earlier session best, but it was insufficient to hold off the relentless Stoner.
The Antipodean's 1min 4.724secs was by far the best time of the day and showed a stark improvement of 2.828secs from his earlier time.
Spies said: "It was a good start today [Friday], the first session I was waiting to see if the track was going to stay the same but in the end in the afternoon it improved a lot.
"We were able to be in the top three in both sessions which is great.
"The track is going to get even better for tomorrow [Saturday] so we're looking forward to making another step forward and seeing what we can do."
Repsol Honda's Dani Pedrosa, last year's winner on the track, was third behind Spies with 1min 41.205secs with his compatriot Jorge Lorenzo, of Yamaha Factor Racing, fourth.
Andrea Dovizioso was fifth while Valentino Rossi failed the crack the top 10 on his Ducati Team ride, coming in 11th.