The Tickford Racing prevailed in hot conditions in the South Australia capital, making up four spots compared to qualifying to take pole.
He did it comfortably, too, his margin back to fellow front-row starter Scott Pye more than three-tenths of a second.
As a result he is now one clear of Will Davison in the battle for most poles this season, with just one more up for grabs tomorrow.
"I needed that pole," said Waters. "I haven't done a clean lap all weekend, but I did it just in time, at the right point.
"I can't thank the team enough, they gave me a really nice car then. It was a bit of a handful until then.
"I'm super pumoped to be starting on the front row. I think we've got a good race car."
Pye's second place came despite a close call in the first corner where he accidentally shifted down to third instead of fourth.
David Reynolds was set to start from third, however his car is being investigated for a technical breach and his position is now pending.
Anton De Pasquale went purple in the first sector before a lock-up at the last corner ruined his lap and he ended up fourth.
James Courtney put his Mustang fifth on the grid ahead of Andre Heimgartner and James Golding.
Provisional polesitter Mostert, meanwhile, missed the set-up window and dropped all the way back to eighth.
"We just didn't quite get the track condition right, and I probably drove a little bit too silly, to be honest," he said. "We'll go back to the drawing board. Long race, I'm pretty confident we've got a good car when we put it together."
Todd Hazelwood will start ninth with Thomas Randle 10th after his missed the cut-off to take part in the Shootout by seconds.
The race starts at 3:15pm local time.
