Whincup and Lowndes finished 10 seconds clear of third-placed Holden driver Fabian Coulthard in the second race.
The four-time V8 champion acknowledged the Circuit of the Americas may prove a significant turning point.
"We were quite off the pace at the start of the year. We were nowhere near the quickest car out there,'' Whincup said.
"Finally now we've got a car which can challenge for wins. We've made a step up.
"All sport all over the world goes in swings and roundabouts. A team at the top generally plummets down to the bottom then comes back to the top three or four years later.
"We're pretty proud of our efforts to stay at a competitive level for a long period of time.''
Whincup now leads Ford rival Will Davison by 113 points in the championship standings after Davison could only manage fourth and ninth in brutally hot conditions.
To compound Ford's difficult day at the office as Holden swept both podiums, fledgling manufacturer Nissan also had something to celebrate.
Rick Kelly's Altima finished sixth in race one - Nissan's highest V8 finish since its return to touring car racing this season.
In the opening race, Whincup powered from second on the grid to pass polesitter Coulthard by the end of the tricky opening turn of the 27-lap event.
Then he held off teammate Lowndes in an engrossing battle for the remainder of the race following pit stops, with Coulthard finishing third.
The second race was far more processional.
Whincup started on pole, held off Lowndes from the start and drove a flawless race with minimal pressure.
Yet again crowds were solid for the V8s' American debut - and featured plenty of curious locals as well as Australians.
Thousands of fans crammed pit lane between qualifying and the first race for a pit walk.
A repeat of the day two crowd on day three should ensure total attendance figures for the event push beyond the 50,000 barrier.
Two more 100km races are scheduled for Monday morning (AEST).