"The track was wet and dry so it was hard to judge the grip," Van Gisbergen said.
"It was good to be driving on a nice wet tyre."
The final race on Sunday was shortened from 46 to 23 laps after a delay caused by a banner strung across the finish line.
High winds caused the banner to flap so violently it threatened to bring two poles crashing down across the track.
Everyone started on slick tyres but rain began to fall on the warm-up lap and Cunningham made the decision to pit before the start to fit wet tyres.
A quick driver change saw Van Gisbergen seize the lead but later his car slowed and Cunningham's co-driver Cameron Waters caught and passed him. The Australian opened a safe gap and brought the Ford home first.
But the pair of Evans and Van Gisbergen were not too disappointed at missing a rare perfect weekend.
"We've won the round and we've got the championship lead - we're buzzing," Van Gisbergen said.
Second overall was Rotorua's Ant Pedersen and Aucklander Jonny Reid, who raced their Ford to second in the final race.
"It was a last-minute effort so we're pretty happy," Pedersen said.
Heimgartner and Morris were third overall although they were only seventh in the final race.
Fourth were young Aucklander Richard Moore with Supercar co-driver Tim Slade, while fifth went to Nelson's John McIntyre - having his first race for the best part of a year - and fast-improving young Taupo racer Mark Gibson.
The BNT NZ SuperTourers endurance series concludes with meetings at Hampton Downs and Pukekohe in November.
