Waters made a perfect start to the race from the outside of the front row, clearing polesitter Davison before getting to the first corner.
He then pulled half a second on Davison and the chasing field across the first lap, only for that advantage to disappear when the safety car was initially called and then the race was red flagged.
The cause of the stoppage was a nasty clash between Scott Pye and Jack Le Brocq as they finished the first lap.
Le Brocq got a run on Pye out of the last corner, Pye then trying to defend his position without realising there was an overlap.
That led to nose-to-bumper contact that spat Pye into the pit wall at speed.
His first point of impact was a gate in the wall which meant the race had to be stopped so repairs could take place.
The race didn't restart for the best part of an hour, Waters picking up where he left off at the front of the field.
Again he could quickly gap Davison, the gap getting out to almost two seconds before Davison peeled into the pits on Lap 23.
Tickford responded on the following lap by pitting Waters who emerged right in front of the DJR Ford.
With his tyres up to temp Davison was then able to get a run on Waters down the back straight before executing a late dive up the inside of the Tickford Ford at Turn 7.
The pair traded paint at the apex before Waters used the old pit entry apron to sweep back in front of Davison and retain the lead.
The controversial move drew the ire of the DJR crew and caught the attention of race control, which handed Waters a five-second time penalty.
Another safety car late in the race, prompted by Will Brown's car shutting down on the entry to the left-hander, made it difficult for Waters to even try and build a five-second gap.
He did get a six-lap sprint at the end but could only get 2s clear of Davison.
That sealed Davison's first race win since the 2016 Bathurst 1000, which was another race where Davison was second on the road, but won thanks to a time penalty for the leader.
It also marked the first Ford win of the 2022 season and the first win for a driver other than Chaz Mostert or Shane van Gisbergen.
"Relief is exactly the word," Davison said of the drought-breaking victory. "You want to earn the wins, so it kind of feels weird not crossing the line first.
"It's just a weight off my shoulders now. I can stop talking about it and we can get on with the business."
The penalty dropped a furious Waters back to fourth in the final standings.
De Pasquale made it a DJR one-two with a solid second stint that included passing Brodie Kostecki at the first corner.
Andre Heimgartner put in a charging second stint to land on the podium thanks to a combination of taking four tyres at his stop and then closing up on those ahead of him behind the safety car.
The Kiwi then had superior grip to work his way into fourth on the road and to within the magic five seconds of Waters.
Van Gisbergen was helped by the late safety car as well with a three-tyre strategy helping him make up plenty of spots in the closing laps as he finished fifth.
That meant he limited the points damage to De Pasquale, his series lead still a healthy 139 points.
Kostecki finished sixth ahead of James Courtney, Broc Feeney, Jake Kostecki and Todd Hazelwood.
