Whincup remains winless for the season but has been runner-up six times and on the podium in nine of the opening 13 races.
"Congrats to Scotty and the crew. They were just too quick today. I couldn't make a race of it," Whincup said.
There was drama on the first turn at the Reid Park street circuit when the Falcon of McLaughlin's teammate Fabian Coulthard spun after Tim Slade nudged him in a congested pack of cars.
It was a cruel blow for Coulthard, who finished 11th and surrendered the series lead to McLaughlin.
While the safety car wasn't called for, Todd Kelly and Slade went to the pits for repairs.
Garth Tander and James Courtney's Commodores also suffered damage early in the race. Kelly later withdrew and Courtney's horror year continued as he was the last to cross the finish line.
In a form reversal for Prodrive Racing Australia, Mark Winterbottom, Chaz Mostert and Cameron Waters finished third, fourth and fifth, respectively.
Defending champion Shane van Gisbergen hung on for seventh, one place behind Triple Eight Racing teammate Craig Lowndes.
McLaughlin will get a chance to consolidate his lead in the 200km race on Sunday.