The Tickford Racing driver inherited the lead on Lap 3 when polesitter Anton De Pasquale slowed with an engine misfire.
He spent the rest of the first stint leading Jamie Whincup before taking his mandatory service for new rear tyres on Lap 12.
While he had the likes of Whincup and Will Davison covered, as usual van Gisbergen emerged as a contender with an overcut strategy.
The Kiwi stayed out until Lap 16 before taking on new tyres on the left-hand side of his car for the run home.
He resumed right behind Waters, the pair staging a tense battle for the lead that went right to the flag.
There was no way through for van Gisbergen though, Waters holding on to win by six tenths of a second.
Speaking post-race he said the win marked a sweet comeback for the Tickford team after his car was destroyed in today’s earlier race.
“I’ve got no words,” he said.
“We had a fast car all weekend. We were quick in the wet and then you know what happened in the first race today.
“The boys worked so bloody hard to fix the car, and not just fix it, but give me one that’s capable of winning.
“The boys earned this one. They gave me a good pitstop and it was up to me.
“We’re really finding a nice window in the car. We were scratching our heads after the last two events. We bounced back this weekend. We had a fast car every session and it’s nice to get one up over him.”
Van Gisbergen added: “What an awesome race.
“We did different things; he did rears, we did the side. We couldn’t quite get him, he drove awesome, put in the car in the right spots and second was where we were.
“It was a good race but again I couldn’t quite get close enough to make a pass. But we’ll take it; good weekend, good points.”
Davison rounded out the podium thanks an undercut strategy that helped him jump fourth-placed Whincup during the stops.
Chaz Mostert finished fifth followed by Nick Percat, who seemed to run out of fuel on the cool-down lap. He was pushed back to the pits by Brad Jones Racing teammate Todd Hazelwood.
Tim Slade finished seventh as James Courtney, Scott Pye and Andre Heimgartner rounded out the Top 10.
Van Gisbergen’s series lead is now 190 points over teammate Whincup.