Waters was battling with Will Davison for the race lead at Wanneroo Raceway when the pair came to blows at the final corner.
It started with a bold dive from Davison down the inside of Waters at the Turn 7 right-hander, Waters then opting to run up onto the old pit entry on the outside and around the exit kerb to retain the lead.
Officials swiftly deemed that to be outside the rules, handing Waters a five-second time penalty for "gaining a lasting advantage upon re-entering the race track".
A subsequent safety car late in the race meant Waters didn't just miss out on the win, but was dumped back to fourth in the final standings.
Both Waters and his Tickford team were furious with the penalty that gave Davison a first win in six years, with team boss Tim Edwards claiming it was "bullshit".
Speaking after his race three win later in the day, reigning champion van Gisbergen came to Waters' defence, arguing that a time penalty was the wrong decision from race control.
He said a redress would have been a better option, with Davison being rewarded for his pass and Waters still able to fight for the lead, or at least second place.
"I complimented [Davison] on his pass on Waters," said van Gisbergen.
"It was an awesome divebomb. I was a little critical of the officials consistency though, I did feel for Cam.
"They could have maybe redressed it straight away, not done what they did. That was pretty rude, I thought."
Waters' team-mate, 2010 champion James Courtney, agreed with van Gisbergen: "I feel for Cam. I feel that it could have been sorted out a bit nicer, I felt the penalty didn't match the crime."
Davison wouldn't be drawn on the severity of the penalty, instead focussing on how he felt he deserved to end up with the lead based on both his passing move, and Waters' decision to use the old pit apron.
"It’s black and white; back in the day, we all used to do that," he said.
"Someone passes you, you get off the brakes and run the speed in, and run around the back of the kerb.
"It isn’t classified as the race track. As we all know in qualifying, you can’t start a lap there or finish one.
"I saw when he cleared the brake and turned in with big speed, I knew what he was trying to do. You would try; but the rule is pretty clear… you can’t do that.
"It was weird. You don’t want to cross the line in second spot.
"I feel like I put a good aggressive move on and deserved the position."
