Van Gisbergen triumphed in the eight-lap opener after a dramatic battle with Anton De Pasquale.
The pair had staged a see-sawing battle, van Gisbergen leading the first stint before De Pasquale ran a lap longer in the first stint.
That helped the Erebus driver emerge with the lead, but it short-lived, van Gisbergen able to reclaim top spot into Les Combes on the same lap. De Pasquale didn't let him go, however, the pair running nose-to-tail in the closing laps.
Their battle then hit overdrive at the Bus Stop on the final lap, De Pasquale drawing level with the Red Bull Holden on the exit. But contact sent the Erebus Holden into the fence, van Gisbergen managing to keep going, but needing to hold off Cam Waters and Scott McLaughlin through La Source – being used as the last corner – to grab a controversial win.
He didn't escape the De Pasquale incident completely unscathed, though. Driving standards adviser Craig Bard slapped van Gisbergen with a post-race rear-of-grid penalty, which will come into effect in the third and final race.
McLaughlin managed to pick up an in-game penalty as part of the La Source panel-rubbing, which dropped him from the podium to 15th, with Waters left in second ahead of Lando Norris.
The McLaren driver made a storming start to the race, going from seventh to four on the opening lap alone. A slow stop then dropped him back behind Waters, a spot he wasn't able to recover across the second stint.
Broc Feeney then won a typically frantic reverse grid race, the Super2 wildcard starting from pole thanks to internet problems in Race 1.
That track position proved key, he and Will Davison running nose-to-tail to take a Tickford one-two, ahead of Garry Jacobson.
Chaz Mostert finished fourth ahead of Race 1 frontrunners van Gisbergen and De Pasquale.
Norris provided one of the more comical moments in the second race, driving backwards up the front straight to get into pitlane after being spun.
He managed to tangle with Chris Pither in the process, Norris' Walkinshaw Commodore left sideways and blocking pit entry.
The Briton wound up a lowly 19th.
He faired better than McLaughlin, though, the Penske Ford driver left with damage after a clumsy Lap 1 move on David Reynolds.
Things went from bad to worse for McLaughlin when he realised he didn't have enough fuel to finish the race, another stop meaning the best he could manage was 21st at the finish.