But he then launched a stunning assault through the field, eventually climbing to third with four laps remaining to ensure his only rival, Mark Winterbottom, cannot catch him at the season's final event in Sydney in a fortnight.
He now holds a 317-point championship lead over Ford's Winterbottom, with only 300 points left on offer this year.
Whincup's Team Vodafone teammate Craig Lowndes won the 67-lap race at Winton, with Winterbottom second.
Whincup, 29, adds this year's title to his 2008, 2009 and 2011 championships. He has won 12 of the 28 races so far this season.
Despite clinching the title, Whincup and Team Vodafone are refusing to celebrate their championship victory until after the final race at Sydney's Homebush.
Only the highly unlikely scenario of a points penalty during the Sydney races for Whincup could in any way reopen the championship, and even then it would be unlikely to be enough to stop him.
"We did it the hard way today," Whincup said of his spirited drive from back to front after his pit lane penalty.
"It's a bit of a dumb rule really [the wheel spin rule] but at the end of the day I broke the rules and have to do the penalty. I'll just bottle the emotion, do everything right in Sydney, and make sure everything is signed, sealed and delivered."
But Winterbottom admitted the title race was over as far as he was concerned, and he was now concentrating on retaining the season runners-up spot with Lowndes still a chance of catching him.
"Obviously the championship is over, but I'd like to split the Triple Eight cars and we're in the right position to do that now," Winterbottom said.
Meanwhile, Chad Reed is confident his horror crash is behind him and he's ready to contend in the US next season after a blistering finish to the Australian Supercross Championship.
The 30-year-old Australian great blazed away from the outset to win the final race in Newcastle by almost 25 seconds from Jay Marmont before 10,000 home town fans.
It capped a super comeback from Reed. His 2012 American season was ruined by injuries, including a torn ACL requiring surgery, received in a high-impact crash in the seventh round of the AMA Supercross series in Dallas in February.
Former world and AMA champion Reed led every lap of the three rounds he contested in the four-event Australian championship, at Phillip Island, Townsville and Newcastle.
It wasn't quite enough to prevent Saturday night's runner-up Jay Marmont from retaining the national title. Marmont needed only to finish on the podium.
But the four-time national champion could hardly have done more and feels his pace is back.
Reed returns to the US on Monday to prepare for the 2013 AMA series starting on January 5 in Anaheim, California, and faces 17 rounds of racing over 18 weeks.
Having switched from Yamaha to Kawasaki, Marmont claimed back-to-back national titles, with Daniel McCoy nine points behind in second and Reed third.
- AAP
