Driving a Richard Childress Racing entry, Brown ended up 0.187s off the pace set by Team Penske’s Ryan Blaney at the end of the 50-minute session, and first of the Chevrolet drivers.
Fellow Cup Series debutant Waters was 35th in RFK Racing’s Stage 60 Ford in the 38-car field.
Brown started his first run with a 1:15.604s and a 1:15.532s in the #33 Chevrolet Camaro but, on his third lap, he jumped to third with a 1:14.875s which was 0.328s off the pace being set by Kyle Larson (#5 Hendrick Motorsports Chevrolet) at that point.
Waters, meanwhile, was a late starter in the #60 Ford Mustang, not hitting the track until around the 10-minute mark.
He gradually crept up to 34th on a 1:16.187s, while also surviving a wild spin through the dirt at Turn 1, where road ringer Boris Said had hit the wall in Xfinity Series Practice.
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Meanwhile, the pace was picking up again and Brown return to the top 10 with a 1:14.594s which put him as high as ninth, 0.476s off the fastest lap belonging to Bubba Wallace (#23 23XI Racing Toyota) at that stage.
Waters started to catch his fellow Supercars driver when he climbed to 23rd with a 1:15.089s on his 11th lap, 1.086s away from the fastest lap.
Brown had been shuffled all the way back to 25th as the session moved into its final 10 minutes but jumped back to seventh with a 1:14.027s which was 0.533s away from Chase Elliott’s (#9 Hendrick Chevrolet) benchmark.
Waters was chipping away, setting a 1:14.829s to sit 31st with four minutes to go.
Alex Bowman, Ty Gibbs, and finally Blaney took over top spot, the latter on a 1:13.202s, as Brown shot back up to third on a 1:13.389s.
The top five in the end was Blaney, Gibbs (#54 Joe Gibbs Racing Toyota) on a 1:13.230s, Brown, Bowman (#48 Hendrick Chevrolet) on a 1:13.420s, and Elliott on a 1:13.494s.
Brown’s RCR team-mates Austin Dillon and Kyle Busch ended up 11th and 15th respectively on a 1:13.706s and 1:13.792s.
Xfinity Series Qualifying starts on Saturday at 15:30 ET/05:30 AEST, with Cup Qualifying later in the day at 18:00 ET/08:00 AEST.