That came after Whincup let Shane van Gisbergen through four laps from home so he could exploit his superior tyre life, the Kiwi then returning the favour by running McLaughlin wide so Whincup could sweep into second.
That opened the door for T8 to swap its two drivers before the finish, which would have handed Whincup an additional eight points over McLaughlin.
However the factory Holden squad opted to leave van Gisbergen out in front, race engineer Grant McPherson telling his driver to "take it to the chequer in this position" on the final lap.
Asked if he felt van Gisbergen should have forfeited the win, Whincup said: “No, I don’t think so.
“[The #97 crew] did a great job with the strategy, it played into their hands. They had four tyres left, so SVG deserved the win and he got it.”
He also defended his decision to let van Gisbergen past in the first place.
“I wasn’t going to hold Shane up. We don’t hold each other up," he said.
“He had some serious pace. When that Safety Car came out he was on for the win so I didn’t want to get in the way of that.”
Whincup currently sits 143 points behind McLaughlin in the standings, with 900 points still up for grabs from the remaining three events.
Triple Eight, meanwhile, holds a slender 42-point advantage in the teams' championship, which determines the pitlane order for the following season.
The first of van Gisbergen's two victories in Townsville helped T8 become the first team to win 200 points-paying races in the top-tier of Australian touring car racing.
The Walkinshaw Racing-run Holden Racing Team outfit racked up 200 wins back in 2011, however that included non-championship rounds such as Albert Park and pre-1999 Bathurst 1000s.
Now running under the Walkinshaw Andretti United banner, the Clayton-based team has 180 points-paying wins to its name.