It was 29-year-old Davison's first win in his second season at FPR.
Whincup, who started from pole position, took the lead from Tander on lap eight around the Adelaide street circuit.
But he struck trouble 37 laps into the 78-lap race, sliding from first to fourth as he complained of an engine miss.
He managed to complete the race without further incident, though his speed appeared curtailed.
Whincup's Team Vodafone team-mate Craig Lowndes had an early setback to his championship hopes after being docked points for an incident in Saturday's opening race.
Stewards confirmed Lowndes, who had finished fourth on Saturday, had been penalised 25 championship points for careless driving following an incident involving Jack Daniel's Racing's Todd Kelly in that race.
Lowndes finished fifth on Sunday.
Holden drivers Greg Murphy and Jonathon Webb failed to make the grid for Sunday's race after a huge crash during the morning qualifying session.
Murphy rear-ended Webb at speed, destroying both cars with neither able to be repaired in time for the race.
Holden driver James Courtney had a wretched weekend, picking up just a handful of points after failing to finish on Saturday and struggling badly on Sunday.
Despite his team working overnight to fix a car badly damaged in a Saturday smash, the 2010 champion was unable to complete a lap during Sunday qualifying - his car stopping midway through his first lap.
He started from the rear of the grid for Sunday's race and was again beset by car trouble, finishing 25th.
More than 82,000 spectators attended Sunday's race - bringing the total attendance for the four days of racing in Adelaide to more than 263,000.
The next round of the V8 championship will be in Tasmania from March 30 to April 1.
