With Whincup closing in rapidly, Davison's car started to cough and splutter with three turns remaining around the Adelaide street circuit.
And Whincup's Commodore rocketed past - Davison just managing to cross the line in second place before his last wisp of fuel evaporated.
Holden's Garth Tander finished third, with Whincup's team-mate Craig Lowndes fourth.
Whincup's win had added emotion after his father David died last Sunday.
Several big crashes at the high-speed turn eight marred the race, leaving many teams facing working overnight to fix destroyed cars for Sunday's second 250km event - including James Courtney's Holden Racing Team.
The 2010 champion wiped out the left-hand-side of his Commodore in a huge lap four incident in which Holden duo Jason Bright and Taz Douglas crashed separately at the same time.
Bright was taken to hospital for precautionary X-rays after complaining of a sore shoulder following the crash.
Ford driver David Reynolds also had a huge crash at turn eight midway through the race, leaving his Bottle-O Racing team an all-night job to repair the car.