From grid 11 in race two, he drove through the pack to second place and took a seven-point advantage over McClymont, Aucklander Nigel Ross and Gisborne's Daniel Cook - who were tied for second - into the third race.
Cowling started at the back of the 20-car grid and raced through to fourth to clinch the title with 56 points from a possible 60.
"There were a couple of hairy moments out by the wall in the last race. I knew it was time to get going and get the job done," he said.
McClymont scored a seventh, third and a win for 52 points and Ross scored 50 to complete the podium.
The runner-up effort extended an unrivalled record for McClymont. In the seven years since Saloon Cars were recognised as a national class, McClymont has always finished on the podium, with his record now at two wins, four second placings and a third last season.
Dan Corrin was fourth on 48 points and Steve Cowling made it all three of the ITM Tauranga team cars in the top five. Tirau's Michelle Wymer was seventh and Tauranga's Neil Head ninth.
Cowling says there's a simple explanation for the Baypark drivers again performing so strongly.
"The competition is really tough at Baypark. We have to race the best of the best every fortnight."
The New Zealand GP will be held at Auckland's Waikaraka Park on February 15 and the North Island Champs at Gisborne on March 22.
