The first stint was a carbon copy of yesterday's race, Waters leading the way as van Gisbergen sat patiently just under a second behind.
And, like yesterday, it was the Kiwi that prompted the pair to make their stops when he took his mandatory service on Lap 15.
Waters predictably responded by pitting the next lap and once again he resumed right in front of van Gisbergen.
This time, however, van Gisbergen was able to use his warm tyres to his advantage, using an impressively late dive to slide under Waters into Turn 3.
Once in front there was no stopping the series leader, van Gisbergen managing the gap to Waters across the final stint.
The final winning margin was 5.2s while van Gisbergen has a 244-point lead in the series.
"It was a great race," said van Gisbergen. "Cam was quick again but our boys did an awesome job in the pitstop and that put pressure on him.
"[We] won the race in the pits and then I put a nice move on Cam. The car was awesome. I just kept pushing.
"He got us yesterday, but I got him back today."
David Reynolds came home third after running long and making some key passes in the second stint.
After running fourth in the first stint, Reynolds didn't take his stop until Lap 22. Initially the undercut left him in fifth behind Will Brown and Chaz Mostert, however it didn't take long for the gripped-up Grove Mustang to barge its way into third.
Lee Holdsworth also worked the overcut in the sister Grove car, the veteran not taking his stop until Lap 24.
He popped out behind the likes of Andre Heimgartner, Mostert and Brown but had the grip to run them all down as he sealed fourth place.
Mostert got by Brown on the final lap of the race as the Erebus driver struggled to get his ancient rubber, fitted during a Lap 5 stop, to the finish.
Brown did, however, manage to hang on to sixth place despite having Heimgartner on his bumper right to the flag.
James Courtney and Mark Winterbottom were eighth and ninth as Anton De Pasquale rounded out the Top 10.
The final heat of the Winton SuperSprint will take place at 3:35pm local time.
Winton SuperSprint Race 2 results
| Cla | # | Driver | Car | Time | Gap | Interval |
|---|---|---|---|---|---|---|
| 1 | 97 |  Shane van Gisbergen | Holden Commodore ZB | - | ||
| 2 | 6 |  Cameron Waters | Ford Mustang GT | 5.298 | 5.299 | 5.299 |
| 3 | 26 | David Reynolds | Ford Mustang GT | 8.542 | 8.543 | 3.244 |
| 4 | 10 | Lee Holdsworth | Ford Mustang GT | 15.057 | 15.057 | 6.515 |
| 5 | 25 | Chaz Mostert | Holden Commodore ZB | 19.916 | 19.917 | 4.860 |
| 6 | 9 | Will Brown | Holden Commodore ZB | 21.830 | 21.831 | 1.914 |
| 7 | 8 | Andre Heimgartner | Holden Commodore ZB | 21.969 | 21.969 | 0.138 |
| 8 | 5 | James Courtney | Ford Mustang GT | 24.826 | 24.826 | 2.857 |
| 9 | 18 | Mark Winterbottom | Holden Commodore ZB | 24.947 | 24.947 | 0.121 |
| 10 | 11 | Anton De Pasquale | Ford Mustang GT | 26.802 | 26.803 | 1.855 |
| 11 | 99 | Brodie Kostecki | Holden Commodore ZB | 27.345 | 27.345 | 0.543 |
| 12 | 88 | Broc Feeney | Holden Commodore ZB | 29.045 | 29.046 | 1.700 |
| 13 | 34 | Jack Le Brocq | Holden Commodore ZB | 40.036 | 40.037 | 10.991 |
| 14 | 17 | Will Davison | Ford Mustang GT | 40.180 | 40.180 | 0.143 |
| 15 | 3 | Tim Slade | Ford Mustang GT | 40.414 | 40.415 | 0.234 |
| 16 | 2 | Nick Percat | Holden Commodore ZB | 40.739 | 40.740 | 0.325 |
| 17 | 35 | Todd Hazelwood | Holden Commodore ZB | 41.950 | 41.950 | 1.210 |
| 18 | 55 | Thomas Randle | Ford Mustang GT | 42.734 | 42.734 | 0.784 |
| 19 | 96 | Macauley Jones | Holden Commodore ZB | 44.957 | 44.957 | 2.223 |
| 20 | 56 | Jake Kostecki | Ford Mustang GT | 45.603 | 45.603 | 0.646 |
| 21 | 14 | Bryce Fullwood | Holden Commodore ZB | 47.278 | 47.279 | 1.675 |
| 22 | 27 | Jayden Ojeda | Holden Commodore ZB | 52.581 | 52.582 | 5.303 |
| 23 | 4 | Jack Smith | Holden Commodore ZB | 57.067 | 57.068 | 4.486 |
| 24 | 22 | Chris Pither | Holden Commodore ZB | 1'03.658 | 1'03.658 | 6.590 |
| 25 | 49 | Jordan Boys | Holden Commodore ZB | 1'08.616 | 1'08.617 | 4.959 |
| 76 | Garry Jacobson | Holden Commodore ZB | ||||
| 20 | Scott Pye | Holden Commodore ZB | ||||
| View full results | ||||||
