"I almost had him [Winterbottom] and I gave it everything I had," said Whincup.
"There were a lot of Holden fans out there who wanted the win. It was a crazy battle and I got very close - so much so I thought I was odds-on to get past him."
Will Davison came home in third and retains his championship lead from Whincup and Winterbottom.
Best of the Kiwis was Fabian Coulthard who picked up two top-10 finishes with his best being fifth in yesterday's race to back up his eighth on Saturday.
"To be honest I'm pretty happy with the weekend. I've got a new engineer for the round and to come out and perform like we did is a credit to everyone who are working as a unit," said Coulthard.
Last year's winner Kiwi Shane van Gisbergen had an average weekend.
"Our car is just not good enough on tracks like this over bumps. On smooth tracks we're good but when we come to a track like this we're just filling the field up. It's still early in the championship and I'm still excited for the season. It's just one tough weekend."
The least said about Greg Murphy's weekend the better. His season hadn't started well with a big shunt, followed by a missed round and a fraught weekend in Hamilton.
At least he salvaged something, with a fighting 17th yesterday.