Whincup ran over an air hose on the way into the box to take his mandatory service, which ripped the air gun out of hands of a crew member.
It then needed to be gathered back up before fitting a new right-rear tyre, a 6.6s stop time dumping Whincup from third to sixth.
The team has now been fined $1500 for the blunder, as well as being docked 30 points in the tense battle for the teams championship with DJR Team Penske.
That means DJRTP's advantage sits at 100 points with just the Bathurst 1000 left to go.
Whincup, meanwhile, went on to finish the race seventh, before conceding the 2020 title to Scott McLaughlin in the final heat after finishing one spot behind the Penske Ford driver in third.