The Tickford driver ran second-last in the Shootout, navigating tricky conditions to bank a 1m14.418s on his single-lap effort.
That left provisional pole-sitter Brodie Kostecki as his only rival for pole, however the Erebus driver could only manage a 1m14.648s that left him fourth on the grid and sealed pole for Waters.
"The track was massively different compared to quali," said Waters. "In quali the track had heaps of grip, it was heaps of fun, but it was pretty loose then.
"I just tried to hit my marks and I knew if I had everything half-okay, I'd be in the mix. The car is great over one lap, we just need to make it work over 88 laps."
Track conditions was a talking point throughout the race, particularly for the those that ran early in the session.
The issue seemed to be a drifting and burnout demonstration right before the session that left a few drivers puzzled by the lack of grip.
Andre Heimgartner and Will Brown even dropped back into the 1m15s as they ended up eighth and ninth respectively on the grid.
Will Davison, who will start seventh, compared it to a gender reveal stunt for expecting parents.
"There's pink burnout rubber everywhere from the burnout cars," he said.
"It's actually pretty dumb, to be honest. You're on the out lap and it's like driving through oil. I was wheel spinning for 100 metres, looking at all this pink and blue."
Jack Le Brocq and Thomas Randle were two drivers that dealt with the conditions well, both making up two spots compared to qualifying as they ended up second and third.
David Reynolds qualified fifth ahead of Anton De Pasquale.
Chaz Mostert was the biggest loser from the session though, tumbling from third in qualifying to 10th on the grid for the race.
The WAU Ford driver didn't even complete his Shootout lap after giving the wall a healthy whack on the way out of turn 2.
The second 250-kilometre race of the weekend kicks off at 2:40pm local time.
