Officials initially showed the black flag to Whincup when the seven-time Supercars champion passed the Safety Car while heading up Mountain Straight.
The incident occurred under the fourth Safety Car for debris on Conrod Straight, and would have seen the 888 entry slip precariously close to dropping off the lead lap.
However, team boss Roland Dane immediately argued the decision with officials, claiming Whincup was waved through by the Safety Car.
“We don't think there is a penalty. He passed the Safety Car when it had the green lights on,” Dane explained when the penalty was initially dished out.
“Two other cars chose not to. They just hung back and hung back so the stewards are having another look at it.
“The Safety Car driver told them what took place. Hopefully they do the right thing.”
Upon review officials elected to rescind the drive through penalty, leaving Whincup to continue in 11th place.
“They've removed the black flag, they've removed the penalty, reversed it,” Dane explained.
“Once they'd had a look at it they realised what had happened.”
Earlier, team manager Mark Dutton admitted the team was struggling with braking issues, with Craig Lowndes revealing there was nothing the team could do and it would simply have to live with the issue.
“We're pushing the brake pedal as hard as we can. The ABS lights are all coming but the retardation of the car is not quite as nice as we'd like it,” Lowndes said.
“We've sort of been chasing it all weekend. Some of the other cars are saying they're fine. We've changed everything in the car, the whole system, the whole ABS system, the whole lot.
“We can't do any more with what we've got. We've got what we've got and we just have to race what we've got.”
Dutton added: “We've got some decent car speed but really the brakes are not working for us as we'd like.”