Having come into the Northern Territory with a 101-point lead over Holden's Craig Lowndes, Winterbottom is now 161 points ahead going into the next round in Townsville.
Lowndes, who had earlier secured his first pole in Darwin since 2000, finished a lowly 17th after damaging a tyre following contact with Ford's Chaz Mostert midway through the race.
Whincup moved up to third on the championship standings, leaping above Fabian Coulthard after the New Zealander struggled to a 22nd-place finish and the defending V8s champion is 186 points behind Winterbottom. Whincup won both 100km races on Saturday from pole position to reignite his bid for a fourth straight title.
He was barely challenged by his rivals in either race, leading from start to finish in both.
After not winning a race since the Tasmania 400 in March, Whincup refused to get too carried away by his dramatic return to form.
"I won't go making any big statements," he said.
"It was refreshing. We had plenty of room for improvement, without doubt.
"The question is, can we continue this for the rest of the year?"
Teammate Lowndes capped his 40th birthday by finishing second in both races.
Standings
1 Mark Winterbottom 1451
2 Craig Lowndes 1290
3 Jamie Whincup1265
4 Fabian Coulthard 1204
5 James Courtney1120
6 Shane Van Gisbergen 1111
7 Scott McLaughlin 1045
8 David Reynolds 952
9 Chaz Mostert 914
10 Jason Bright 881
-AAP
