The Kiwi left his run late in in the second-half hour session, jumping to the top at the flag with a 1m44.838s.
That was the best part of two seconds faster than Anton De Pasquale's benchmark in the first session as the Supercars field adapts to the new-look Albert Park layout.
Van Gisbergen's lap edged James Courtney by just 0.08s, the veteran having led the way for much of the session.
He did improve on his final run to be one of just two drivers to dip into the 1m44s bracket.
Chaz Mostert was third fastest after a quiet first session followed by Dick Johnson Racing pair De Pasquale and Will Davison.
Rookie Thomas Randle was an impressive sixth despite running wide at the last corner on his first lap.
Scott Pye and Nick Percat were next while Jake Kostecki rounded out a good session for Tickford with the ninth fastest time.
Cam Waters was the only Tickford car not to make the Top 10, his best time only good enough for 14th and he battled with brake issues.
There are two qualifying sessions to come today which will determine the grids for Races 1 and 2.
