Whincup strengthened his bid for a sixth series crown with two wins from three races at the Townsville street circuit, cutting the FPR-Ford man's advantage for a second straight weekend.
HRT-Holden driver Garth Tander also enjoyed a stellar performance at the Queensland venue, winning once and finishing second to Whincup in the other two outings.
In the opening contest poleman James Courtney (HRT-Holden) retained the lead at the start while Craig Lowndes (Triple Eight-Holden) made contact with Tander, before Courtney was nudged into the wall and Scott McLaughlin (GRM-Volvo) grabbed the lead.
He built a healthy advantage, but when the safety car was deployed following a crash for Lowndes, McLaughlin was at the mercy of Whincup. He lost P1 in the pits, handing Whincup a lead he would not relinquish. Tander took second ahead of Will Davison (Erebus-Mercedes), while McLaughlin slid to sixth.
Fabian Coulthard (Brad Jones-Holden) started from pole in race two and held his spot at the front. However the HRT machines were making quick progress through the pack after qualifying down the grid, and a mistake from the leader allowed both Tander and Courtney to scythe through.
The order stayed that way to the chequered flag, while Whincup claimed solid points in P7.
He was back at the sharp end for the weekend’s concluding race, using an alternate strategy to claim the win. While most of the pack pitted during an early safety car period Whincup stayed out, a choice that would prove crucial late on.
As the race reached its concluding stages Whincup was second to Tander, but his fresher rubber allowed the Triple Eight man to catch and pass the HRT with relative ease.
Tander held on to second, while Shane van Gisbergen (Tekno-Holden) snatched the final podium spot from Courtney in the dying stages.
It was a less successful weekend for championship leader Winterbottom. The FPR driver could only manage 11th in the opening race, eighth in the second and sixth in the third, costing him points to Whincup in every outing.
That has allowed Whincup - who has now won four of the past six races - to get within 100 points of his rival. Behind them by some distance there is an intense battle for third, with Coulthard, Van Gisbergen, Courtney and Lowndes separated by a minuscule nine points.
The series’ next event takes place at Queensland Raceway over the weekend of August 2/3.