Several drivers fell by the wayside in the 84-lap classic; Andrew Thompson was sent spinning into the wet grass rounding the Turn 5 sweeper, before Dean Fiore and Tony Ricciardello came to blows at the back of the circuit. Both incidents triggered the Safety Car.
Will Davison also struck drama on lap 32, with his Holden Racing Team Commodore hemorrhaging oil and causing many in the trailing pack to slip up.
With a championship at stake, title hopefuls look fondly on the races they win when their closest rivals falter.
For Winterbottom, he stood taller than ever on a day all three of his championship rivals hit trouble.
Courtney was penalised for contact with Lee Holdsworth, and was consigned to a second finish outside the top 10 in as many days.
Whincup loomed to clinch a top five finish, only to be forced in for a late fuel stop. The reigning champion finished 15th, and on a day he was meant to close the deficit widened to 50 points to Courtney.
Lowndes, though, suffered the most of the quartet, after challenging for the lead early on, the #888 Commodore slumped to the rear with a gearbox issue. He would fail to finish the race, and the deficit to Courtney blew out to 257 points.
Winterbottom celebrates a well-earned win
"That was a very satisfying and hard-fought win today,” Winterbottom said.
"The car was very good in the wet, so I blazed early. However, when it dried I had a bit of understeer and it turned into a hard-fought win.
"Both Jason Bright and then Paul Dumbrell really did push me all the way today, plus we went to the dry tyres maybe a lap or two early because of the Safety Car.
“Then the drizzle was still about and a HRT car dumped oil, so we had plenty going on.
"Although the car had a lot of understeer going into the hairpin especially, it actually gave me good exit speed and that was important in holding the others off down the long straight.”
Winterbottom, now with Team 18, will return to Symmons Plains for the Beaurepaires Tasmania SuperSprint across April 10-11. Tickets are on sale now.
The event will be broadcast live on Foxtel and will be streamed on Kayo.