There was a heated battle between the pair in the closing stages of the race, both drivers making contact with the other as van Gisbergen executed a classic overcut strategy.
In the end the result went the way of van Gisbergen, who logged a first Gen3 win after having his Saturday victory taken away due to a technical breach.
That Saturday disqualification for van Gisbergen means Mostert leads the series after the opening round.
It was Mostert that made the swiftest start, the Walkinshaw Ford driver jumping David Reynolds from the outside of the front row to take an early lead.
His charge only last several corners, though, the safety car called just moments after the start due to a clash between Declan Fraser and Macauley Jones on the front straight. Fraser looked to turn across the front of Jones as they pulled away from the grid, which resulted in the Tickford rookie being fired head first into pitwall.
The subsequent damage to the barriers led to the caution becoming a red flag so that repairs could take place.
The race resumed under the safety car on lap 3 before going green at on lap 5, Mostert leading Reynolds, Cam Waters, James Golding and van Gisbergen.
That was the order for much of the first stint until Mostert hit the lane for his first stop on lap 23.
It wasn't until six laps later than Waters did likewise, followed by Reynolds a lap later, which dropped him back behind both the Monster Mustang, and an early-stopping Broc Feeney.
Around the same time van Gisbergen passed Golding on track before setting off on a long first stint.
The Kiwi didn't make his first stop until lap 38, resuming in fifth behind Reynolds, until Reynolds was able to clear Feeney for third. By lap 46 van Gisbergen would also get past Feeney, although at that point he was still 17s behind the leaders.
The gap at the front was closer, though, with Waters pulling up right behind Mostert on lap 47.
A lap later Waters pushed slightly too hard into Turn 9 in pursuit of Mostert, clipping the inside wall and bending a steering arm. He took his second stop on lap 49 with the crew undertaking lengthy repairs on the arm, which took him out of contention for the win.
Two laps later there was another change near the front of the field, van Gisbergen taking over second on the road from Reynolds at the last corner.
Van Gisbergen had also worked the gap to Mostert down to 10s as he used his much fresher rubber.
The Kiwi continued to work down that gap until Mostert stopped for new tyres on lap 58.
Reynolds was the next to stop on lap 68, a slow stop due a wheel issue and some set-up changes dropping him to fourth behind Golding. He was able to work his way back past the PremiAir Camaro thought to reclaim the final spot on the podium.
Van Gisbergen then made his final stop on lap 70, resuming around eight seconds behind Mostert with a timed out finish looming.
The pair then picked their way through lapped traffic as they bolted to the flag, van Gisbergen closing to within three seconds as the race entered its final 10 minutes. With the traffic cleared van Gisbergen was able to properly use his tyre advantage, the gap down to within a second with five minutes left.
The race peaked several laps later when van Gisbergen nudged Mostert wide at Turn 9 to take the lead.
Mostert did his best to fight back at the penultimate corner as he returned serve on van Gisbergen, however while the Kiwi ran wide he still had the line for the final corner and retained the lead.
Once in front he had to the grip to bolt clear, crossing the finish line 4.4s clear of Mostert. Reynolds came home third ahead of Golding and Feeney.
Brodie Kostecki was sixth from Andre Heimgartner and Jack Le Brocq, while Tim Slade and Mark Winterbottom rounded out the top 10.
Waters dropped back to 12th after his brush with the wall, while for the second day running neither Dick Johnson Racing Ford made the top 10, Anton De Pasquale 16th and Will Davison 19th.
The Supercars season continues at Albert Park on 31 March-2 April.
