Percat stayed out until the end of lap 12 and did enough to negate the undercut from the likes of Coulthard - delayed by a right-front problem - emerging just ahead in what was effectively fourth.
He caught Mostert, who was then among the group of drivers to pit for wets.
James Courtney crossed the line in fourth, but lost that place to Tim Slade due to a five-second penalty incurred for a mid-race clash with Craig Lowndes at Turn 10.
For his part, Lowndes crossed the line in sixth, ahead of Mark Winterbottom, Will Davison and Cameron Waters.
In 10th, Mostert was the first driver home on wets, the long pitlane a factor in his final 39.8084s deficit to Pye.
Coulthard was 12th in the lead Shell V-Power Racing Falcon, three spots ahead of team-mate McLaughlin, who had radio problems and had to double-stack during the extra stops.
Championship leader Shane van Gisbergen and David Reynolds were 13th and 14th, while Michael Caruso was the lead Nissan in 16th and 18th-placed Todd Hazelwood - who did not pit for wets - the top rookie.
During the late pitstops, Garth Tander came unstuck on the slippery surface and made contact with his crew, and finished last, while team-mate James Golding had a pair of spins in the wet on his way to 24th.
Richie Stanaway split them, having served a drive-through penalty for pitlane speeding during his stop for wets.
The final race at Albert Park, and decider in the fight for the Larry Perkins Trophy, will be held at 1:45pm on Sunday.