Waters led Payne through the opening stages of the race before the Grove Ford driver pitted on Lap 19 for a stop that included serving a five-second jump start penalty.
The Tickford ace pressed on for another six laps before pitting and emerging back on track with the Penrite Mustang closing in at full speed.
Waters initially weaved back and forth to warm his tyres, before appearing to make a late final dart to the inside as Payne arrived.
Payne backed out to narrowly avoid contact but was less than pleased with his rival’s actions.
“I was sort of waiting for him to make his intentions clear on where he was going to go,” Payne recounted to Speedcafe.
“Obviously, he was weaving a lot, so he hadn’t made his mind up of what he was going to do, from my point of view.
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“I had already committed to the inside being the safer option and it looked like after I’d made my decision, he made his decision, which ended up making it quite dangerous.
“It’s frustrating when he’s weaving out of the pits, I’m coming down the straight a lot quicker and not knowing what he’s going to do.
“I made my move and then he reacted to that when it’s should be the other way around.
“It was good we didn’t crash, we could still carry on, but I wished we were another five car lengths up the road so we could have cleared them.”
Waters, who eventually finished second to Kai Allen, said he was “very surprised” to receive a bad sportsmanship flag for moving in the braking area.
“I’m not sure why I got it, to be honest. I need to ask the stewards,” he said.
“Obviously they think I deserved the bad sportsmanship flag. I didn’t think anything of it. You come out of the pits, you weave a little bid, and I blocked.
“I’m sure he would have been complaining about how dangerous it was. It was obviously very dangerous from his position.
Payne, who finished fourth, said he retreated from the move due to fear that turning Waters around would draw a penalty.
The situation left the race as a case of what might have been, with Payne optimistic that a win could have been on if he’d taken the track position.
“I thought our car was really good in clean air,” he said.
“It could have changed the race a lot. It could have been a possible win or a podium for us that went begging.”
Payne’s early pit strategy had largely been dictated by his jump-start penalty, which he admitted had been a clear breach.
“I thought the lights have been a little bit inconsistent this weekend to normal,” he said.
“Today I saw the Carrera Cup race they held them on really short, but for us it was really long.
“I just started to lose the clutch and then basically got to the point where the car was ready to go but the lights were still on.
“So I couldn’t stop it from happening. I don’t know if we got an advantage from it, but the rules are the rules.”
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