Holden's Nick Percat was third. Remarkably, Davison never led at any stage of the 56th Great Race.
"It ran out of fuel as I crossed the finish line - I can't believe the way it panned out."
Neither could Whincup - or Red Bull Racing.
Whincup copped a 15 second time penalty after trying to snatch second spot from Volvo's Scott McLaughlin on lap 150.
He made contact with McLaughlin at The Chase, forcing the Volvo driver off the track.
McLaughlin weaved back onto the track, spectacularly crashing with Holden's Garth Tander.
Red Bull Racing appear confident after coughing up $10,000 to lodge the protest.
"The penalty they gave is completely inconsistent," Red Bull team boss Roland Dane told supercars.com.
"It is questionable whether Jamie was guilty of any crime when you actually look at the incident with McLaughlin.
"(But) the stewards have confirmed that the 15 seconds penalty is nothing to do with the aftermath.
"That wasn't Jamie's fault."
A Supercars spokesman said: "A date has yet to be set to hear the appeal.
"The results of today's race are final but subject to the appeal."
Six-time Supercars series champion Whincup said he would apologise to both drivers.
"But I felt the move was on," he said.
He didn't get much sympathy.
"Whincup started all that," said Tander. Tander's team owner Ryan Walkinshaw was more scathing.
"A @holden-racing Bathurst win robbed from us with 10 laps to go by two people running out of talent who should know better. Gutting," he tweeted.
Whincup had looked like the man to beat, breaking the race lap record three times before fate stepped in.
Van Gisbergen still leads the Supercars series on 2248 points ahead of Whincup (2241) and Craig Lowndes (2091).
Davison is in sixth spot after his second Bathurst win.In the end, eight of the 27 cars failed to finish prompting six safety cars.
The biggest name scalp was Ford's Mark Winterbottom whose brakes failed on lap 135. The defending series champion remained at fifth in the drivers' standings.
There was also no luck for sentimental favourite and defending Bathurst champion Lowndes. The Holden veteran had hoped to claim a seventh Bathurst to honour Peter Brock on the 10th anniversary of his mentor's death.
He finished fourth-last after his campaign was sabotaged by early gear issues.
- AAP