He finished fourth, ninth and 12th in the weekend's other races.
That allowed Whincup to skip away to a 142-point championship lead, and teammate Lowndes to leapfrog Davison into second place on a successful weekend for Red Bull Racing.
Holden driver Fabian Coulthard won race three in the only respite from Whincup's domination in the sport's first foray into the US.
Lowndes was second and Whincup third in that race, but stewards were probing a possible mid-race breach by Coulthard which could cost him the victory.
Stewards said Coulthard was under investigation over failing to maintain his speed at a restart following a safety car period - a breach of race rules.
Whincup had won the two races on Sunday.
In a dismal weekend for Davison's Ford Performance Racing, teammate Mark Winterbottom had his hopes of winning race three cruelled by a botched pit stop.
A problem changing the rear tyre cost Winterbottom the race lead, and plunged him to seventh.
It followed a similar horror pit stop at the previous round in Perth which cost Winterbottom multiple positions.
- AAP