The Team 18 driver went quickest on his final run, courtesy of a move to a set of green Dunlops after focussing on race laps earlier in the half-hour session.
A 1m06.240s was good enough to leave him a tenth clear of Bryce Fullwood and Lee Holdsworth.
"I think the most promising thing isn't only the last lap, but what our pace was like on the used tyre," said Pye.
"I think it's okay. It was a fairly scrappy lap. There's probably 5.9 or a 6.0 in it if I put it together. There's plenty fo come from me and a bit of tuning with the car as well."
Cam Waters spent most of the session on top after an early 1m06.625s, but slipped to fourth after only improving to a 1m06.469s on his final run.
Chaz Mostert and Rick Kelly were next, with Jack Le Brocq, Macauley Jones, Andre Heimgartner and Garry Jacobson rounding out the Top 10.
Most of the usual front-runners concentrated on race runs rather than Hollywood lap times, with Shane van Gisbergen the best of the 'big two' teams down in 12th.
Points leader Scott McLaughlin was just 18th quickest, while Triple Crown winner Jamie Whincup was 20th.