Waters got congratulations from all of his rivals for his first win in the category after making huge improvements to his driving this year.
"I don't know what to say - I am so pumped," he said. "This guy [Stanaway] did a bloody mega job - got me the lead and I managed to hold onto it."
Championship leader Scott McLaughlin banked a vital second place, along with co-driver Alex Premat, as some of his title rivals ran into problems and he will take a 84-point lead into next month's Bathurst 1000.
Chaz Mostert and Steve Owen completed an all-Ford podium.
Championship contender Fabian Coulthard and co-driver Tony D'Alberto finished fifth, collecting valuable points to help the Kiwi's title aspirations as others missed out.
Reigning series champion Shane van Gisbergen endured a chaotic day in his Red Bull Holden. He was handed a two-place grid penalty for contact with Coulthard in practice and opted to buck the trend of starting the race in the car while the majority of the field went with co-drivers.
It was a stunning display of aggressive driving including going from 21st to 13th on the opening lap. He stormed to the lead of the race by the end of his first stint. Co-driver Matt Campbell maintained the speed and van Gisbergen looked to be on track for a podium in the latter stages of the race when a tyre let go with 25 laps remaining. He finished in 16th as a result.
Teammate Jamie Whincup's title challenge was dealt the same blow when co-driver Paul Dumbrell had a tyre explode on him while in the lead of the race. It appeared the tyre was damaged from excessive curb use. He dropped to the back of the field as a result before Whincup set foot in the car. The pair fought back in the second half of the race to finish sixth and salvage a decent haul of points.
David Reynolds also suffered a similar issue in the Erebus Racing Holden, ruining what had been an impressive weekend to that point.
The tyre situation is becoming a huge embarrassment for the sport - the Dunlop 2017 tyre has failed on a far too regular basis as teams are forced to de-tune their cars to protect from blowouts. The 2016 version will be in use next up at Bathurst and again at Pukekohe later in the year with those high-degradation tracks considered too risky of a serious accident.
The race was halted for over an hour after only a couple of laps when a Taz Douglas crash caused damage to the safety barriers. Cars lined up on the grid while the problem was fixed.
Championship Standings
Scott McLaughlin 2334
Jamie Whincup -84
Fabian Coulthard -161
Chaz Mostert -282
Shane van Gisbergen -420
