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"One hundred per cent that was against our advice and that's just not clever."And that is disappointing that we didn't manage the fuel as well as we could have done."
Whincup was unapologetic for running with his own strategy and was happy he put on a "good show".
"There were two options in my head: conserve the amount of fuel they wanted me to conserve and run second, or go all out and try and win the race," he said.
"We went all out and ended up finishing fifth."
Whincup started the Great Race in 23rd and produced one of the drives of the day to charge his way into the top five in just 15 laps.
Jamie Whincup. Photo / Getty Images
The result has kept him on top of the overall standings and in line for a record sixth V8 Supercars championship.
Things didn't work out as well for his teammate Craig Lowndes, who was relegated to 10th on Sunday after clipping Ford's Mark Winterbottom with 11 laps to go.
He copped a drive-through penalty for causing the incident, which ended both their chances of victory.
Lowndes admitted it was his mistake, blaming the sun glare, and said he spoke to Winterbottom after the race.
It marked just the second time in a decade that Triple Eight Race Engineering, racing as Red Bull, has missed the podium at Bathurst.
"We win or lose collectively as a team and there were other aspects we didn't do well enough and will have to improve," Dane said."We were fast enough to have a one-two and it's our fault we didn't."
-AAP