Red Bull Racing Australia left the Skycity Triple Crown with mixed emotions after its domination of the hard tyre sprint races failed to translate to Sunday's 200km soft tyre finale.
The result marked Whincup's first race win since Symmons Plains in March and followed what the team described as a much-needed test day at Queensland Raceway earlier this month.
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The pair again locked out the front-row on Sunday and appeared to be in the box seat for victory after an early Safety Car played into the hands of their tyre strategy.
A misjudgement from Lowndes in traffic soon caused a puncture for the #888 Holden however, ensuring a lowly 17th placed finish.
Whinup eventually finished third after proving unable to match the soft tyre life of his Ford Performance Racing and Tekno Autosports rivals in the closing stages.
“There's no doubt about that we've made up ground,” Lowndes told Speedcafe.com of the team's progress since the previous event in Perth
“We came into the weekend without having a pole position at all (at Hidden Valley).
“For Jamie to have two on Saturday and myself to have one as well it's a clear sign that we've stepped up.
“But we need to keep stepping up. FPR have good tyre longevity in their soft tyre runs.
“We need to look at that, especially going into the long distance races.”
The 40-year-old admitted that his mistake on Sunday was particularly disappointing after a sterling qualifying performance had seen him take pole while saving a set of brand new tyres for the race.
“It was disappointing because we had a great opportunity to maximise,” he said, having fallen 161 points behind FPR's Mark Winterbottom in the championship fight.
“We started off pole and had a brand new set of tyres for the end, but with that puncture we had to put one of the four on early and that front-left did a stint and a half.
“We were just too far back in the end to do anything.”
Whincup is now third in the points standings, 186 adrift of Winterbottom after a mixed run through the opening 19 races.
Echoing Lowndes' thoughts on Red Bull's need to improve on the soft tyres, the five-time champion believes that returning to the top of the podium on Saturday was an important moment in his season.
“It was really, really important,” he said of winning on Saturday.
“We had a good test day, we were fairly off the pace in New Zealand and also Perth.
“We've bridged the gap but there's still a bit to go.
“We're confident of our pace on hards but there's plenty of soft rounds coming up so that's obviously where our focus will be in the next few months.”
The balance of the season is then made up of one soft tyre (Gold Coast), one mixed tyre (Sydney Motorsport Park) and four hard tyre (Sandown, Bathurst Phillip Island and Sydney) events.