The Tickford driver was consistently near the front throughout the half-hour session, having led the way early with a 1m12.995s – the first time under the 1m13s mark.
He was pipped by David Reynolds at two-thirds of the way through the session by 0.001s, before the pair were shuffled back in the final five minute 'happy hour'.
But a switch to green rubber vaulted Waters back to the top, his 1m12.503s on his final run good enough to put him 0.18s clear of Shane van Gisbergen.
"[The car] rolled out pretty good," said Waters.
"It's a little bit different to what we finished with in Darwin, it's more towards out street circuit car. We bolted [the set-up] in and it worked, it's pretty close.
"It's still not perfect, and it's only Practice 1 so the track is still coming up. It's a good start but there's still a long way to go this weekend."
Jamie Whincup finished the session right behind his teammate in third, as Bryce Fullwood used green tyres to jump up to fourth on his final lap.
James Courtney, Rick Kelly and Jack Le Brocq were next, as Reynolds slipped back to eighth after not running greens at the end.
The two Penske Ford drivers concentrated on race runs in the session, Fabian Coulthard just 21st fastest and Scott McLaughlin 22nd. The points leader did, however, cover more ground than anyone with 21 laps.
|2||97||Shane van Gisbergen||1'12.692||0.189||0.189|
|7||55||Jack Le Brocq||1'12.952||0.449||0.043|
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