Initially it was Brodie Kostecki that led the way courtesy of a 1m49.059s on his first run.
He was then displaced by Cam Waters mid-way through the session as the times dipped into the 1m48s bracket.
Inside the last 10 minutes van Gisbergen made his move, pulling clear of the field with a 1m48.260s.
The series leader then went out for another run right at the flag, setting purple sectors in the first and second sectors before falling away in the third.
Still, his earlier time was good enough to leave the Kiwi just over a tenth clear of title rival Anton De Pasquale in the final times.
Waters ended up third after improving to a 1m48.379s on his final run, followed by Chaz Mostert and Tom Randle.
Kostecki dropped back to sixth as the qualifying sims shook out ahead of Mark Winterbottom and Practice 1 pacesetter Broc Feeney.
Tickford wildcard Zak Best kept his impressive start to the day going with the ninth fastest time as Will Davison rounded out the Top 10.
The grid for today's opening race will be set by a three-part qualifying session starting at 1:30pm local time.
