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 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 has grown to 108 points.
More to follow.