Winterbottom misjudged his approach into turn one - the same corner that cost him in Saturday's earlier race - allowing Whincup to swoop past.
Craig Lowndes overtook Winterbottom on the following lap, giving his teammate a crucial buffer.
With superior pace, the Red Bulls ran away with the race, completing a one-two result ahead of Winterbottom and handing Whincup the crown.
Whincup said while he wouldn't get the trophy until the final meet in Sydney next month, there was plenty of emotion on the grid.
"Points wise, it's all done," he said.
"That trophy's going to be pretty sweet come the end of the year."
While Whincup moved past five-time champions Ian Geoghegan, Dick Johnson and Mark Skaife to be the only man with six crowns, he said he was not thinking about his place in the sport's history. "The numbers are one thing, I'm sure they're going to mean a hell of a lot when I hang the helmet up," he said.
"Hopefully that's not for a long time yet.
"Right now I'm in the heat of the battle, and never loved my motorsport than I do right now."
Red Bull's strong day - both drivers finished on the podium in both races - means the constructors' championship is also all but guaranteed to head their way.
Whincup's 2014 title is provisional - there remains the very unlikely possibility of stewards' punishment or suspension.
But his 461-point lead is now greater than the maximum points on offer from the four remaining races,and on form, no one could catch him anyway.
The 31-year-old has blitzed the field since ending an 11-race run without a win in Darwin.
Whincup's incredible streak since his visit to the Northern Territory is: nine victories and 13 podiums from 18 races.
Saturday's earlier race was claimed by Scott McLaughlin ahead of Lowndes and Whincup.
Lowndes' pair of second-place finishes on the coastal circuit lifted him above van Gisbergen into third in the championship standings.
-AAP
