For the second day running Whincup was untroubled across the 39 laps, converting pole to a win without conceding the effective lead at any point.
He was particularly strong across the first stint, Whincup able to gap second placed Chaz Mostert by more than six seconds before stopping on Lap 22.
Mostert did manage to halve Whincup's advantage around the stops, but the seven-time champion was able to comfortably manage that gap in the second stint.
The final margin between the two was right on three seconds.
"The car was fantastic," said Whincup. "I got good start and had a good battle with Chaz into Turn 2.
"From there the car was excellent. We don't normally go long, we normally go pretty short. It was great to go long and have some good tyres for the end there."
The top two were in a league of their own, Shane van Gisbergen finishing a hefty 16 seconds behind his Red Bull Holden teammate in third.
That was thanks to a rapid second stint, the Kiwi charging past the likes of Scott McLaughlin, Cam Waters and James Courtney to seal the final spot on the podium.
Waters and Percat finished fourth and fifth, while McLaughlin completed a decent recovery from 13th on the grid to finish sixth. That was largely thanks to impressive tyre life, McLaughlin stopping early but still able to mix it with the likes of Percat at the end.
Whincup's win did still put a dent in McLaughlin's series lead, though, the gap now 109 points.
Courtney ran third for much of the race, but a rear locking issue in the last 10 laps proved costly as he slipped all the way back to seventh.
Anton De Pasquale was best of the Erebus Holden in eighth, two spots ahead of teammate David Reynolds, while Scott Pye made up 10 positions to finish ninth by running long and then having the good rubber for the last 12 laps.
Townsville Supercars - Race 2 results:
|1||88|| Jamie Whincup ||Holden Commodore ZB|
|2||25|| Chaz Mostert ||Holden Commodore ZB||3.014|
|3||97|| Shane van Gisbergen ||Holden Commodore ZB||16.131|
|4||6|| Cameron Waters ||Ford Mustang GT||20.439|
|5||8|| Nick Percat ||Holden Commodore ZB||23.789|
|6||17|| Scott McLaughlin ||Ford Mustang GT||24.365|
|7||44|| James Courtney ||Ford Mustang GT||28.637|
|8||99|| Anton De Pasquale ||Holden Commodore ZB||29.104|
|9||20|| Scott Pye ||Holden Commodore ZB||29.839|
|10||9|| David Reynolds ||Holden Commodore ZB||30.222|
|11||5|| Lee Holdsworth ||Ford Mustang GT||31.298|
|12||55|| Jack Le Brocq ||Ford Mustang GT||31.833|
|13||14|| Todd Hazelwood ||Holden Commodore ZB||33.564|
|14||7|| Andre Heimgartner ||Ford Mustang GT||34.381|
|15||12|| Fabian Coulthard ||Ford Mustang GT||39.634|
|16||35|| Garry Jacobson ||Holden Commodore ZB||41.489|
|17||18|| Mark Winterbottom ||Holden Commodore ZB||43.741|
|18||3|| Macauley Jones ||Holden Commodore ZB||43.944|
|19||2|| Bryce Fullwood ||Holden Commodore ZB||45.719|
|20||15|| Rick Kelly ||Ford Mustang GT||47.010|
|21||34|| Zane Goddard ||Holden Commodore ZB||52.108|
|22||19|| Alex Davison ||Holden Commodore ZB||52.491|
|23||4|| Jack Smith ||Holden Commodore ZB||54.433|
|24||22|| Chris Pither ||Holden Commodore ZB||55.237|
|View full results|