The Tickford Racing driver was consistently quick across the 15-minute session, going to the top early with a 1m19.669s.
That time was eclipsed by Shane van Gisbergen's 1m19.368s at the end of the first runs, but Waters was able to reclaim top spot with a 1m19.109s on his final run.
That secured provisional pole for Waters, who will be looking for a benchmark 11th pole of the season in the Top 10 Shootout.
Anton De Pasquale ended up second fastest courtesy of his final run while Chaz Mostert was another later improver, popping up in third.
Van Gisbergen slipped back to fourth after not improving on his second run, however the Kiwi was still happy after starting yesterday's race from last.
"It's pretty good. Better," he said. "The car is still pretty hard to drive, but we're in the show this time, which is good.
"Hopefully I'll stay somewhere in the front half of the 10 for the race it will make things a bit easier than yesterday."
Will Davison was fifth fastest followed by Will Brown, Andre Heimgartner and Broc Feeney.
Todd Hazelwood booked an emotional spot in the Shootout on what is his final day as a Matt Stone Racing driver. Adding to the emotion was that his MSR crew was at the track until after 3am repairing Hazelwood's Holden after his crash with Waters in yesterday's race.
"It's awesome, a great reward for the whole team," said Adelaide local Hazelwood. "We were here until half past three this morning trying to get the car fixed up after yesterday's melee.
"To stick the car in the Shootout after that hard work is a great feeling.
"Sometimes you've got to use frustration in a good way. It's fuelling the hunger today. Hopefully I can repay the team today after a result went begging yesterday."
David Reynolds was the final driver to book a Shootout berth after a late effort from Jack Le Brocq fell 0.001s short of 10th spot.
The Top 10 Shootout kicks off at 12:05pm local time.
