"At the end of the day we're going to be one or two but two would be pretty devastating with how the year has panned out so we won't leave any stone unturned."
Whincup has mixed feelings about the final two venues.
"I like Sandown and grew up in Melbourne so I've done a lot of Formula Ford racing there and I'm familiar with the track," he said.
"But, unfortunately, no Team Vodafone car has got anywhere near the podium at Sydney - if it's still tight we'll go there with the best opportunity for both drivers."
Team boss Adrian Burgess said there would be no team orders despite Whincup's leading position and both he and Lowndes would be allowed to race unrestricted.
Whincup on Sunday capitalised on a mistake by polesitter Paul Dumbrell in Sunday's 84-lap race to seize the lead and hold on to win by 1.7 seconds from Ford driver Will Davison.
Ford's Mark Winterbottom finished third while Dumbrell was fourth, one spot ahead of Lowndes.
Ford team-mates Dumbrell and Winterbottom claimed the front row after qualifying and Dumbrell, on pole, led for the opening 20 laps.
However, Whincup pounced when Dumbrell made a basic error running off the track after exiting from a pit stop.
At one point after taking over the front running Whincup became nervous when a persistent noise in the car developed.
"We had a little rattle in the car from midway on so I was very nervous that was going to bite me," Whincup said.
"Luckily though it didn't get any worse and we were able to get to the end."
Davison moved up to become Whincup's closest challenger with Winterbottom and Dumbrell scrambling to stay within sight.
Lowndes, meanwhile, had been unable to come to grips with the car during qualifying and started from a lowly 15th on the grid.
He battled his way up through the field, but had given away valuable points to Whincup, who increased his championship chances dramatically.