It was an anti-climax to the title fight with the weather stopping van Gisbergen from sealing the deal with a win.
Van Gisbergen heads into the season ending Bathurst 1000, beginning December 3, with an unbeatable 349 point lead over Whincup.
"It sucks that we couldn't put on a show," van Gisbergen said. "But it has been an awesome time and super cool to win another championship."
While some will say the championship was gifted to him when Scott McLaughlin relinquished his crown by switching to Indy Car, van Gisbsergen led from start to end to win the title with a full round to spare.
The Kiwi driver also took out the Sydney Cup.
"We haven't been fast enough this year but we have gotten the results and been consistent," van Gisbergen said.
"We haven't made the mistakes that the others have. We had one bad race but we were up there for the rest of them."
Van Gisbergen will now chase the greatness he seemed certain to achieve after winning his first title in 2016.
After accounting for Whincup and seemingly ending his record-breaking reign, most thought the Kiwi was about to begin a period of domination to rival his teammate.
But Whincup rebounded to even further his own legend by claiming his 7th crown in 2017.
Van Gisbergen's march to become an immortal was again derailed in 2018 when Scott McLaughlin arrived onto the V8 scene in his thunder stealing Ford.
McLaughlin went on to claim three straight crowns before quitting the sport.
While some will claim the former DJR/Penske super-star would have made it four had he not gone off to chase his American dream, van Gisbergen's name is now etched on the championship trophy twice.
"It is my life dream and my life goal," van Gisbergen said. "I won the first one and just wanted to do it again. Now I want to do it again. It is an awesome feeling.
"I want to keep racing here as long as I can. It seems a while ago that I won my first one so it is a very cool feeling."