Starting second, Reynolds had out-dragged polesitter Whincup off the line, moving down the inside of the Red Bull entry into the first corner.
Percat pounced on the exit, undertaking a deft switchback on Whincup to move into second by Turn 3.
The trio ran line astern across the opening laps, with just 1.2 seconds between them when the Safety Car was called to retrieve James Golding’s Holden on lap eight.
Golding pulled his Garry Rogers Motorsport Commodore off at the exit of Turn 2 having lost oil pressure, requiring the full course yellows for three laps.
That left just one racing lap before the time cut-off, with Reynolds never looking seriously threatened for the win.
“It was a pretty good race,” smiled Reynolds, who had criticised himself for giving away a win in Adelaide earlier this month but not driving aggressively enough.
“I got a good start and kind of just led the race from there. Everything went from there, there was no dramas.
“From the battle we had yesterday in the wet and dry conditions, it was a good way to finish.”
While Reynolds finished just 14th in the dry-wet race yesterday evening, today’s result marked Percat’s second podium in 24 hours.
“The BJR guys have done a mega job since Adelaide,” he said.
“We knew we had a fast car from the test day, we had to rectify a few things.
“Awesome few days, my best weekend with BJR by a long way, and in Supercars by a long way.
“Normally it’s been a bit with spikes and stuff like that, but all weekend, never had a session out of the top 10.
“I think the Safety Car hurt us, we were coming and just waiting for his rear tyre [to go off] but two podiums in one weekend, I can’t complain.”
Whincup took the inaugural Larry Perkins Trophy for being the highest points-scorer across the weekend, but was left disappointed by his start in the finale.
“Sweet and sour at the moment,” he said.
“I’m just filthy with myself for a shocking fourth race, just muffed the start.
“But to grab the Larry Perkins Trophy, obviously we did a good job, the best job over the weekend so we’ll take that.”
Chaz Mostert and Scott Pye ensured the top five finished as they started, while Scott McLaughlin improved from ninth to sixth – passing team-mate Fabian Coulthard in the process.
Coulthard appeared to let his faster team-mate through on lap seven before going on to finish seventh, while Michael Caruso, Garth Tander and Will Davison rounded out the top 10.
Championship leader Shane van Gisbergen was the hard charger, taking eight places on the opening lap as he sliced from last to an eventual 13th.
Van Gisbergen maintains his position atop the standings, while Reynolds moves back into second with his victory, 49 points behind.
With their weekends, Scott McLaughlin and Jamie Whincup moved from fifth to third and 18th to sixth, respectively.
James Courtney had made it from 25th to 19th on lap one before being hit from behind and spun by Golding at Turn 3 on the second tour.
A blind-sighted Rick Kelly tagged the stationary Holden, putting both cars out of the contest, while Lee Holdsworth also pitted for repairs after being caught up in the melee.
“It was a cracking opening lap with Shane, it was really good to get through,” said Courtney.
“Unfortunately I was on the end of a conga-line there and got spat out at the end. It’s the way it happens, I guess, when you’re starting in that position it can happen.”
Mark Winterbottom and Cameron Waters ran 15th and 16th before the Safety Car, under which they took new tyres and dropped to 20th and 21st.
With just one racing lap to make up places, they could do no better than 17th and 18th on the road at the end, before Waters was demoted to 22nd thanks to a five-second time penalty for early contact with Anton De Pasquale.
De Pasquale kept his Holden off the wall following the Turn 10 touch and went on to finish as the top rookie in 15th.
The 2018 Virgin Australia Supercars Championship continues with the Tyrepower Tasmania SuperSprint at Symmons Plains Raceway on April 6-8.