Cooper had to be content with finishing 3-2-3 as he was locked in a fierce fight with Coppins and Carter for the remaining podium spots.
"It was a great event," said Townley. "The weather was against the organisers all night, but we got racing started late in the afternoon and the crowd certainly seemed to enjoy it.
"Winton Motorcycles were amazing. I only arrived on Wednesday. They were so helpful.
"I've only been on a bike five or six times over the past few weeks, so my fitness is not at its best."
The battle for senior 250cc (lites) class honours was a see-saw battle between Australian visitor Richard Evans and Tauranga-based former Rangiora rider Micah McGoldrick.
They ended up sharing the overall results. Evans scoring 1-3-2 and McGoldrick 2-1-3, although Evans got the nod on the countback rule over McGoldrick.
Balclutha's Madison Latta won the junior 250cc title and Matamata's Brodie Connolly won the junior lites title.
Meanwhile, Ashburton Andrew Rudd coped best with the wet and blustery conditions to win the New Zealand Hill Climb Championships that were staged earlier in the day as part of the Burt Munro festival.
He took his Honda CRF450 motard to clock 51.66secs on his second of three runs to claim both the up to 600cc class and overall fastest time.
Leading final standings after the New Zealand Supercross Championships at Winton:
Senior open: 1. Ben Townley (Tauranga, Suzuki) 60 points (maximum); 2. Cody Cooper (Mount Maunganui, Honda) 47; 3= Josh Coppins (Motueka, Yamaha) and Rhys Carter (Mount Maunganui, Kawasaki) 43.