McLaughlin minimised the damage by completing the podium with veteran Craig Lowndes fourth and Ford's Chaz Mostert fifth.
A safety car came with 18 laps remaining and that was the ticket for the Red Bull Holden outfit.
McLaughlin and Craig Lowndes had already taken their final stops so it brought Van Gisbergen right into the hunt and while Whincup had to double stack he was able to get the time back behind the safety car.
Fabian Coulthard ended up 11th having started alongside McLaughlin on the front row.
Richie Stanaway was 21st while Andre Heimgartner's race was ruined with an early mechanical failure.
"It took a long time for that race to come alive – it was pretty stale and the safety car came out and it was awesome," Van Gisbergen said.
"Scotty was driving really well, he defended awesomely. I gave him a couple of bumps and he wasn't fazed. Unfortunately I think he had some pick up and we got back through.
"A really awesome weekend."
McLaughlin cut a dejected figure after the race after it looked like he had the race under control with 20 laps remaining.
Despite the disappointment, McLaughlin still holds a healthy lead in the standings.
"I tried so hard to keep them behind," McLaughlin said. "Great strategy call by them – well done to Shane and well done to Jamie and sorry to the Ford fans that I couldn't get it done for you. I am absolutely gutted.
"We had a great car today; I have a great team, great pit stops, great strategy but unfortunately that safety car came at the wrong time.
"I am stoked, a good point's day and we will move on."
The championship moves to new South Australian track Bend Motorsport Park in three weeks.