Whincup set an imposing benchmark at the outset of the 20-minute session, with a 1:49.6498s on his first flying lap.
That was the quickest time of the weekend, and had Whincup six tenths clear of van Gisbergen, with Craig Lowndes completing an all-Triple Eight top three.
Whincup did not improve on his subsequent runs, but it did not matter, and he claimed a 79th career Supercars pole and fourth of 2018.
Van Gisbergen improved late, trimming Whincup's final margin to 0.4017 seconds.
Late efforts from Tim Slade and Scott Pye put the South Australians third and fourth, in their Freightliner and Mobil 1 Boost Mobile Commodores.
Whincup said he was particularly fired up for the session after being forced to double-stack on his way to fourth in Saturday's race.
“[Engineer David] Cauchi and the crew made the car better today and I got the most out of it, plus a little bit of a tow off my team-mate as well, which resulted in a '48, so I’m very happy,” Whincup said.
“I was a bit gutted after yesterday. We worked so hard to get a result and then someone robbed the till halfway through the race and we ended up P4 [after double-stacking].
“There was a little bit of anger there, but we came out strongly today.”
Fourth for Pye marked a big improvement from Walkinshaw Andretti United, after starting 23rd on Saturday.
“I think our car didn’t deal with the conditions well yesterday, but today we’re back to where we were in practice, or maybe a bit further ahead,” he said.
“I was thinking we’d maybe be ninth, or 10th, but we’re well positioned.
"We’re on the right side as well, yesterday I think starting from the inside was a bit of a disadvantage.”
Nissan's Michael Caruso, fresh from taking his first podium in two years on Saturday, slotted into fifth place.
Slade, Pye and Caruso demoted Lowndes to sixth, but that still proved a stark improvement from the Autobarn Holden's 25th on Saturday.
James Courtney, top rookie Anton De Pasquale, Rick Kelly and McLaughlin completed the top 10.
McLaughlin was seventh after his first run and improved to fifth with his second, but could not find more time on his third, winding up 1.0347s off Whincup's benchmark.
“We thought we made some gains, the car felt better but we just didn’t improve over the session,” McLaughlin said.
“I felt the lap was ok, but I just didn’t get the gain we look for on a green tyre normally.
“It’s what it is. We’re 10th and we’ll just have to fight on from there.”
Fabian Coulthard's Shell V-Power Racing Falcon was 13th, ahead of the best of the Tickford Racing Fords, Cameron Waters in 14th.
Tickford's other entries, driven by Mark Winterbottom, Chaz Mostert and Richie Stanaway - who had a spin at Turn 14 - will start 17th, 24th and 27th.
Wildcard runners Macauley Jones and Kurt Kostecki managed 20th and 26th, with Todd Hazelwood rounding out the 28-car field back in Matt Stone Racing's Holden.
Sunday's 41-lap race OTR SuperSprint race starts at 1:40pm local time.