It was polesitter Will Davison that got the jump at the start as van Gisbergen slid down the inside of David Reynolds to nab second place.
The Kiwi then quickly put the blowtorch to the back of the race leader, shadowing Davison until Turn 6 on the second lap where he slipped past with a neatly-executed move.
Once in front he was able to gap the Shell Ford, pulling 1.5s clear before the safety car was called on Lap 5 when Andre Heimgartner was spun by Will Brown at the last corner.
That sparked a flurry of stops, van Gisbergen able to take his mandatory service, switch to the hard compound tyres and continue in the lead.
Reynolds, who had taken his stop right before the caution, was able to jump Davison, while the big loser of the stops was Anton De Pasquale, who had been fourth but dropped to 20th after being forced to double stack, and then stalling on his way out of his box.
The race went green again on Lap 8, Davison dropping another spot when he was shuffled wide by Brodie Kostecki, which let James Courtney through to third.
But there was worse to come for Davison, who copped Cam Waters' Tickford Mustang in his bumper on the approach to Turn 3 on Lap 10.
That left him beached in the gravel and prompted the second caution of the race.
When the race went green on Lap 13 van Gisbergen was able to swiftly gap Reynolds, the Kiwi then cruising to a 2s win ahead of the Grove Ford to extend his championship lead.
The battle for third turned wild after the restart, with Courtney coming under immense pressure from Chaz Mostert.
Their squabble came to blows on the very last corner of the race, Mostert tipping Courtney into a spin, and subsequently the wall, as they bashed doors.
That let Lee Holdsworth sneak through to put two Gove Racing cars on the podium.
Courtney got going again but finished ninth while Mostert was fourth on the road but slapped with a post-race pit-lan penalty that dropped him to 22nd.
That left Scott Pye in fourth ahead of Todd Hazelwood, while Garry Jacobson was a fine sixth place for the new PremiAir Racing squad.
Kostecki ended up seventh ahead of Tim Slade, Courtney and a recovering Anton De Pasquale.
The Melbourne 400 continues with the third race later today.
