The race got off to a dramatic start after second-row starter Anton De Pasquale was shuffled to the back end of the Top 10 in the first few corners.
He then made contact with Brodie Kostecki on the exit of Turn 6 which fired the Shell Ford into the wall.
However there was an even bigger impact at Turn 10 when Will Brown clashed with Mark Winterbottom and hit the wall hard.
The race was red flagged due to the a concrete wall near pit entry being shifted by the crash, while medical crews had to work on a winded Brown trackside before he was transferred to the medical centre.
Supercars later confirmed that Brown wasn't seriously injured while Winterbottom was hit with a pit-lane penalty for his role in the incident.
The race got back underway on Lap 6 with van Gisbergen initially leading Will Davison.
However a failed attempt to wrangle the lead from van Gisbergen on the outside at Turn 8 on the restart lap proved costly for Davison, who was run wide and dropped back to fourth behind Chaz Mostert and Cam Waters.
Van Gisbergen continued to lead by around a second until the lead group started their stops when Waters pitted on Lap 16.
Mostert and Davison followed suit a lap later before van Gisbergen covered them all off the next time round, the top four resuming in the same order.
They stayed that way until the time certain finish too, van Gisbergen ensuring the Pukekohe farewell will feature at least one Kiwi victory as he crossed the line 2.3 clear of Mostert.
"I could see it when I got the start, and then on that last lap," said van Gisbergen of the enthusiastic local crowd.
"What a feeling, I'm going to miss this place.
"It was a bit crazy on the restart, I did everything I could to get going. I was struggling with my tyres but then once it cleared up I was gone."
Van Gisbergen leads the Jason Richards Trophy heading into the final ever Supercars race at Pukekohe this afternoon.
Scott Pye finished Race 2 fifth behind Waters and Davison, with Andre Heimgartner sixth, David Reynolds seventh and Broc Feeney eighth.
Jake Kostecki put in a solid effort to finish ninth ahead of James Golding.
