What was meant to be a half-hour session marked the debut for the new Gen3 Supercars on the fast, flowing Melbourne parklands circuit.
Drivers all started out on the hard compound tyres, Winterbottom leading the way on the first timed run with a 1m51.017s.
That was swiftly eclipsed by Anton De Pasquale who set a 1m50.467s in his Shell Mustang, before Tim Slade enjoyed a very brief stint on top Tim Slade courtesy of a 1m50.341s.
Moments later van Gisbergen went fastest with a 1m50.174s, that time still the benchmark when the session came to an abrupt halt.
The culprit for the stoppage was Slade who ended up on the exit of Turn 5 with a badly damaged PremiAir Camaro.
The crash was instigated when he lost the rear on the way into the corner, the Chevy slapping the outside wall at speed before coming to a rest on the inside of the track on the approach to Turn 6.
The session went green with just over 10 minutes to go, De Pasquale jumping to the top with a 1m50.119s.
He was then pipped by Winterbottom's 1m49.967s which came moments before van Gisbergen sparked a second red flag.
The reigning series champion dropped a rear wheel on the outside of the fast right-hand Turn 8 which sent him into multiple spins before he clipped the wall.
With all Supercars sessions time certain this weekend that proved to be the end of any running, leaving Winterbottom on top ahead of De Pasquale and van Gisbergen.
Waters ended up fourth fastest from David Reynolds, Will Davison, Brodie Kostecki and Slade, who was still eighth despite what he described as a frustrating crash.
"It's massively frustrating," he told Fox Sports. "We're all a bit gun shy with these cars for the first time here at this circuit.
"It felt relatively good but I wasn't pushing, I hadn't gone flat through any of the fast stuff. I actually stuffed up a couple of corners before and I short-shifted one corner, I was going to come into the pits, short-shifted the next corner and before I knew it the rear had gone. It was gone from the entry and completely disconnected and into the wall.
"I'm sorry for everyone in the team."
Practice continues with a second half-hour sessions at 1:15pm local time.
