Fellow New Zealander Fabian Coulthard (Lockwood Racing Holden) drove well to move through the packed field from 17th on the grid to finish 11th and retain his spot in the top-10 in the championship.
Whincup overcame an early race spin to win race four of the championship and move back into second place behind Will Davison on the ladder, now just 18 points adrift.
The TeamVodafone driver started from fifth on the grid and after making early ground, he spun on lap seven. Whincup moved back through the field and withstood a late battle with Van Gisbergen to claim the 54th win of his career.
"We had a tough weekend all in all so to come away with that I'm a little bit shocked," said Whincup, who led home five Fords to claim his eighth race win at Symmons Plains - the most of anyone in the championship history.
"It's crazy how this sport works. Nothing went right all weekend and we walk away with a third and a win. I don't want to dwell on the negatives but we'll improve on that. Lucky enough in the spin I nailed it and spun it around!"
Trading Post FPR Ford pilot Davison finished third - but not without drama.
"It was a bit tougher than yesterday's race," he said in a race where he clashed early with pole-sitter Craig Lowndes, the damage putting the TeamVodafone driver out of the race.
"It was a shame to have a touch with Lowndes. I knew he was behind me, I didn't really know where he was. I just felt the hit and that was that."
Stone Brothers Racing had a strong day with Tim Slade fourth and Lee Holdsworth sixth, separated by Winterbottom, who lost his momentum when he stalled during his second pit stop.
New Zealand fans will now look to the streets of Hamilton for the next stop in the V8 Supercars Championship calendar - albeit for the final time - with the hope of iconic kiwi driver Greg Murphy can recover from back surgery last week to take his place on the grid.
