After starting 24th – due to a van Gisbergen DNF in the second Saturday sprint race – Tander ran longer than the majority of co-drivers as he blitzed through the field, making up 22 places in 72 laps before jumping out.
The deeper strategy opened up the chance for van Gisbergen to gradually close the gap to Whincup, requiring shorter fuel stops through the back half of the race.
Van Gisbergen passed Whincup moments before the latter peeled in for his final stop on lap 134.
The Kiwi emerged from his own pitstop two laps later with a 10-second buffer, but just as a third straight Red Bull one-two finish loomed, van Gisbergen’s Commodore gave way at the right rear.
The 2016 champion tried to carry on before having to give up the fight with 10 laps remaining, pulling into the pits for repairs that would ultimately put him two laps down.
That loss was Tickford Racing’s gain, with Chaz Mostert/James Moffat and Lee Holdsworth/Thomas Randle moving up to be a distant second and third.
Mostert appeared set to deny Holdsworth his first podium in 2045 days when he passed The Bottle-O Mustang on lap 136, before trouble struck for van Gisbergen.
For Mostert meanwhile, it was a nice bounce back from a terrible endurance swing, including missing both Gold Coast races after a qualifying shunt.
McLaughlin finished ninth after being relegated to the back of the grid for its controversial Bathurst engine breach.
McLaughlin and Alex Premat ran quietly in the midfield for much of the day but did enough to put the title beyond doubt a round early in a rather circumspect manner.
They were issued a 15-second time penalty along the way for a refuelling infringement at their first pitstop.
The sister Shell V-Power Racing Ford of Fabian Coulthard/Tony D’Alberto recovered from being spun by Richard Muscat early to place fourth, ahead of Scott Pye/Warren Luff for Walkinshaw Andretti United.
In welcome dry conditions, Lowndes held fellow front-row starter Bryce Fullwood behind off the line, while other co-drivers had trouble getting away.
Alex Davison stalled, dropping from fourth to the back of the field; D’Alberto and Will Brown also losing massive ground immediately.
Among the fast starters was Jake Kostecki, who rose to fourth before enduring an eventful run of events.
The 19-year-old collided with Luke Youlden, bumping the Penrite Holden wide, then had contact with Chris Pither upon exiting his pit bay, and finally rubbing panels with Michael Caruso, whose Monster Energy Mustang was damaged after bouncing off the wall.
The #56 wildcard entry escaped punishment for any of those incidents and went on to finish 16th.
The other major moment during the co-driver stint was a high-speed accident between Dale Wood and Youlden on the back straight.
Wood had looked to put a move on Richard Muscat ahead, with Youlden moving to the inside of both – only to get tangled up with Wood and trigger the Safety Car.
The latter did eventually return to the track, more than 30 laps down, while the Youlden/David Reynolds Commodore was ruled out of action, ending a disappointing PIRTEK Enduro Cup campaign.
Pye was the only primary driver to start the race and made up tremendous ground before handing over to Warren Luff to continue on an alternate strategy.
No one impressed more than Tander though, who picked off cars one-by-one and then was helped by the timing of the lap 32 Safety Car.
From there, the battle quickly became a two-horse race between the Red Bull Holden Racing Team cars.
As it turned out, Whincup and Lowndes would take their fifth and sixth Sandown 500 win respectively and sew up the PIRTEK Enduro Cup.
"Obviously commiserations to #97, they did a great job today, but at the same time we've been on the receiving end of that one as well many times," said Whincup.
"Big thanks to CL [Craig Lowndes], he's done an amazing job all season of endurance and great to be in victory lane."
Added Lowndes: "We had a great car all weekend, Jamie and I had a really cracking day yesterday.
"Got away to a reasonable start, but Shane for #97, they came from the back of the grid to the front and it's sort of happy and sad at the same time."
Will Davison/Alex Davison were sixth, with James Courtney/Jack Perkins seventh and Andre Heimgartner/Fullwood taking eighth despite a 15-second penalty for speeding in pitlane.
Anton De Pasquale/Brown rounded out the 10 behind McLaughlin.
Along with Youlden/Reynolds, there were two other non-finishers: James Golding/Muscat, and Garry Jacobson/Dean Fiore.
The championship now heads to Newcastle for the series finale across November 22-24.