Payne languished in 18th position on the starting grid, but he and co-driver Garth Tander worked their way through the field in a race marred by horrific wet conditions that claimed several contenders along the way.
Fellow Kiwi Ryan Wood was among them, limping to the pits with 20 laps remaining, after briefly poking his nose ahead.
Payne also spun off the track, as he challenged Cooper Murray for the lead with nine laps left, slipping back to third, but benefitted from a collision between Murray and James Golding to edge past into the lead with five laps remaining.
Golding was assessed a five-second penalty for his part in the incident and, although he went ahead again on the last lap, Payne managed to stay within the required margin to win on corrected time.
"I saw Jimmy get into the side of Cooper and I kind of predicted that was going to happen. I managed to get through, but felt like I ran out of tyres at the end.
"A win's a win and we'll take it."
Veteran Tander captured his sixth Bathurst crown - his two most recent came with Kiwi Shane van Gisbergen in 2020 and 2022.
"Something about tall Kiwis at Bathurst," Tander beamed. "He [Payne] kept away and kept his calm, and even managed that last lap, when Golding was mucking around with his five-second penalty.
"That was a seriously impressive drive, really happy to be part of it."
Payne, 23, has now won four Supercars races this year and six across his career, joining a distinguished list of Kiwi winners at 'The Great Race', including van Gisbergen (3), Richie Stanaway, Scott McLaughlin, Greg Murphy (4), Steven Richards (5) and dad Jim Richards (7).
