The Red Bull Holden driver made a smart getaway from pole to charge into a lead he wouldn't surrender across the 39-lap journey.
He already had a handy margin when he made his sole mandatory stop on Lap 17, taking on three new tyres before cruising to a 6.8s win.
That was despite no communication with the pitwall after Lap 10, that, combined with Whincup being unsure if he'd seen the chequered flag on the last lap, leading to him pulling up on the front straight rather than pitlane after the finish.
"We lost radio about Lap 10, I was screaming at the guys to put the [pit] board out," said Whincup.
"And then I din't get the chequered flag; he sort of had it out but he didn't know if it was me or not. I remember the old man said to keep going until you get the chequered flag, so I kept going. I was just trying to wing it with no radio.
"All in all I'm happy with the win, the car was excellent. We used three tyres, I think most maybe only used two. But we needed a win when we could grab it."
Cam Waters finished second after running longer than most in his first stint.
The Tickford driver didn't make his mandatory stop until 23 laps from home, using his fresher rubber to quickly close in Chaz Mostert, who'd stopped seven laps earlier.
The pair staged a brief, intense battle before Waters blasted past at Turn 11 four laps from home.
"I had a bit of fun coming back through the pack, and racing Chaz as well," said Waters. "We actually kept it clean, which is amazing for us two..."
Mostert added: "It was a good old battle for Cam, we just had nothing for him. I wish I could have put on more of a show."
Fabian Coulthard got by David Reynolds late in the race to grab fourth, while Scott McLaughlin came all the way from 16th to finish seventh behind James Courtney.
The series leader made nearly all of his positions on the first lap, a classic Lap 1, Turn 2 concertina crash wreaking havoc on the midfield.
McLaughlin was able to sneak through, despite copping a whack on his rear bumper, emerging in eighth.
Converting that to a seventh place finish limited the damage to his series lead, his advantage still 141 points over Whincup.
The likes of Anton De Pasquale and Shane van Gisbergen weren't as fortunate in the first-lap crash, the former able to recover to 10th while the latter lost nearly 10 laps for repairs on his Red Bull Holden.
Chris Pither was the surprise of the race, the Team Sydney driver right in the midfield battle as he finished a well-crafted 11th.
Townsville Supercars - Race 1 results:
|1||88|| Jamie Whincup ||Holden Commodore ZB|
|2||6|| Cameron Waters ||Ford Mustang GT||6.885|
|3||25|| Chaz Mostert ||Holden Commodore ZB||13.667|
|4||12|| Fabian Coulthard ||Ford Mustang GT||20.969|
|5||9|| David Reynolds ||Holden Commodore ZB||22.714|
|6||44|| James Courtney ||Ford Mustang GT||29.345|
|7||17|| Scott McLaughlin ||Ford Mustang GT||32.853|
|8||2|| Bryce Fullwood ||Holden Commodore ZB||34.662|
|9||20|| Scott Pye ||Holden Commodore ZB||41.499|
|10||99|| Anton De Pasquale ||Holden Commodore ZB||41.575|
|11||22|| Chris Pither ||Holden Commodore ZB||41.870|
|12||18|| Mark Winterbottom ||Holden Commodore ZB||42.714|
|13||5|| Lee Holdsworth ||Ford Mustang GT||43.758|
|14||35|| Garry Jacobson ||Holden Commodore ZB||46.292|
|15||55|| Jack Le Brocq ||Ford Mustang GT||1'02.613|
|16||4|| Jack Smith ||Holden Commodore ZB||1'02.889|
|17||15|| Rick Kelly ||Ford Mustang GT||1 lap|
|18||19|| Alex Davison ||Holden Commodore ZB||1 lap|
|19||97|| Shane van Gisbergen ||Holden Commodore ZB||9 laps|
|8|| Nick Percat ||Holden Commodore ZB||16 laps|
|34|| Zane Goddard ||Holden Commodore ZB||19 laps|
|7|| Andre Heimgartner ||Ford Mustang GT||22 laps|
|14|| Todd Hazelwood ||Holden Commodore ZB||32 laps|
|3|| Macauley Jones ||Holden Commodore ZB||38 laps|
|View full results|