The field was almost perfectly split in terms of tyre strategy for the opening 20-lap race, with 13 cars starting on the soft tyre and 12 on the hard.
There was perfectly represented at the front of the field, where the likes of David Reynolds and Mostert started on the soft and Anton De Pasquale and Will Davison started on the hard.
That made life easy on polesitter Reynolds at the start, although Mostert was able to clear the DJR cars at the first corner to make sure he stayed on Reynolds' bumper.
It quickly became evident that the WAU car was quicker than the Grove Mustang, Mostert passing Reynolds to grab the lead at the last corner on lap three. From there Mostert comfortably led the first stint until pitting to switch to hard compound tyres on lap seven.
By that point both DJR cars had already pitted for softs, which gave them the undercut needed to jump Mostert, with De Pasquale (in on lap four) leading Davison (a pit caller on lap three).
But the early stops made it difficult for the DJR drivers to keep their softs alive and Mostert duly caught them with nine laps to go, first passing Davison for second before taking the lead from De Pasquale at Turn 11 two laps later. From there, Mostert was free to cruise to a 7.6s win.
"I don't think many people expected the race to be what it was," said Mostert.
"Strategy helped our race. We went aggressive and it ended up being the safer option.
"I'm just happy, any time you win in this category it's amazing. We weren't that strong through practice and qualifying but the car is getting faster and faster."
Things only got worse for the DJR cars in the closing stages of the race as they tried to nurse the softs to the end.
Davison was quickly caught and passed by Reynolds before deciding to make a second stop to change back to hards, which dropped him to 16th at the finish.
De Pasquale, meanwhile, suffered a puncture with four laps to go and ended up way down in 23rd.
Reynolds held on to second place at the finish, although he did so under some pressure from van Gisbergen, who was badly caught out by a red flag in qualifying caused by Jake Kostecki crashing his Tickford Ford at Turn 5. The Kiwi had returned to pitlane after copping a kerb strike on his first lap, and didn't get out in time before the red flag.
But van Gisbergen put in a masterful drive from the very back of the grid to end up third thanks to some sharp strategic work and excellent on-track passing.
Starting on the softs, the defending champion went from dead last to 16th on the first lap and was inside the top 10 by lap five.
He then jumped onto the hard tyre for the second stint and continued his march forward. The podium winning move came on Mostert's WAU team-mate Nick Percat with a couple of laps to go, sealing the remarkable comeback following his qualifying dramas.
Tim Slade ended up fourth after also getting through Percat at the end, while Macauley Jones put in a very solid drive to grab sixth place.
Mark Winterbottom was seventh followed by Broc Feeney, Garry Jacobson and Bryce Fullwood.
Van Gisbergen now leads the championship by 129 points over De Pasquale, with Mostert in third, 131 points adrift.
The Melbourne 400 continues with two 20-lap sprint races tomorrow.
