An alternate strategy of starting on the soft tyres helped Lowndes recover to fourth in the race itself, while Whincup emerged with a hard fought seventh.
With only a slim bank of pre-marked tyres available to practice on, team manager Adrian Burgess told Speedcafe,com that the team had simply been underprepared heading into qualifying.
“Where we are at the moment with the tyre rules it's difficult coming to every event with good tyres in your bank,” he said.
“We came here with average tyres and did an average job with them.
“We didn't do a good enough job in practice and arrived in qualifying with a car that wasn't good enough and needed some tuning.
“Clearly in the race we had to roll the dice with one of the cars because if you do the same thing with both of the cars and a Safety Car comes at the wrong time one car is clearly going to be affected.
“It was a no-brainer that we split them and it made sense to do it with #888 as he had a better chance to make the most of it.”
Whincup added that it was only on the hard tyre, which is compulsory for qualifying on both Saturday and Sunday, that the team has been struggling on.
“On the hards we just couldn't do anything, but on the softs, the car is miles better,” said the four-time champion.
“We have struggled all weekend on hards – we qualified poorly on hards and struggled in the race. Then we put the softs on and they transformed the car.
“It just shows how important set-up is. I've got the best prepared, best built, fastest car out there but if you don't get the set-up right you're mid pack.”
Although stressing the competitiveness of the championship, Burgess is quietly confident of a Sunday revival following a long night analyzing data from the 70 lap race.
“We've still got some work to do to tune it up for qualifying tomorrow but we've got some good info and know the direction we need to go,” he said.
“After the race they (the drivers) both had the same comments about the soft tyre and the same comments about the hard tyre.
“That's a good thing from an engineering point of view. They're both singing from the same hymn sheet which gives us a good direction.
“We're not just stabbing in the dark, we know what we've got to address. We'll work hard tonight and hopefully come out tomorrow in a better position.
“It's not an easy championship. Today just showed that there are other good teams and engineers in the paddock that do a good job.”