The Kiwi was only headed in the first few laps of the race before taking control of the 36-lap affair.
He expertly managed his tyres on the high-deg Sydney circuit to come home comfortably ahead of Andre Heimgartner and Anton De Pasquale.
The win moves van Gisbergen into third in the standings, 13 points ahead of teammate Broc Feeney and 54 behind leader Brodie Kostecki.
Will Brown is still second, 41 points behind Kostecki.
Having fumbled the lead from pole last night, Heimgartner made a perfect getaway from the outside of the front row today.
He used the grippier side of the track to charge into an early lead, although his first-lap advantage was as good as it got.
A change in the lead was immediately inevitable, though, as van Gisbergen stalked the leader.
On lap 4 he made his move, cleanly executing a move on Heimgartner at turn 6.
By that stage one title contender was already at the back of the field, Brown taking a high-speed excursion through the dirt at the first corner.
The Erebus driver found himself on the outside of a three-into-one situation with Anton De Pasquale on the inside, and David Reynolds in the middle, as they argued over seventh place.
De Pasquale was the only one to get through unscathed, both Reynolds and Brown flying off the track and rejoining at the back of the field.
Van Gisbergen made light work of the first stint, pulling 7s clear of Heimgartner.
Behind the top two there was a tense wrestle over third between Feeney and Kostecki.
It took until lap 15 for Kostecki to finally muscle his way past, which prompted Feeney to pit for new rubber at the end of the same lap.
Kostecki waited until lap 18 to make his stop, the undercut dropping him back behind Feeney, as well as the early stopping De Pasquale and Bryce Fullwood in the order.
Heimgartner made his stop on lap 19, he too resuming behind Feeney and De Pasquale.
Van Gisbergen responded with a stop of his own the following lap, his advantage enough to ensure he resumed in the effective lead.
With teammate Feeney the next in the queue the job was straightforward from that point on for van Gisbergen.
By the time Heimgartner had worked his way through De Pasquale and Feeney, van Gisbergen was in cruise control with a 3s lead.
The Kiwi then managed the gap over his countryman, eventually crossing the line 5.2s to the good.
That led to him quipping that he wanted at least a five-second lead following his penalty at the end of yesterday's race.
"I have to thank the team so much," said van Gisbergen.
"They haven't given up on me. I've been struggling a bit but they've rebuilt this car [and] changed the chassis, they've done so much work.
"It's so cool to be back here [in victory lane]. Back on the right track.
"I've never driven so slowly to win a race. At the end [the gap] was three seconds and I thought I better get to five seconds in case they penalise us again."
Heimgartner was a somewhat lonely second, while Feeney and De Pasquale staged an epic late battle for third place.
De Pasquale was rapid across the second stint, closing in on third-placed Feeney as the laps counted down.
He then got through on the final lap of the race to complete the podium and win the Mustang Cup on a day where just three Fords made the top 10.
That dropped Feeney back to fourth ahead of Bryce Fullwood.
Kostecki never really recovered the ground lost around the stops and even lost more in the closing stages as he battled clutch dramas. That dropped him back to eighth behind Ford pair Cam Waters and Chaz Mostert.
After his lap 1 woes, Brown was able to work his way back to 14th at the finish.
Reynolds couldn't make the same progress, the Grove Racing driver finishing 20th.
