Having won race 2 earlier today despite crossing the line behind Joey Mawson, there was no doubting his victory in race 3.
The Versa Motorsport driver dominated the 12-lapper, the critical moment coming at the start.
That was when he held his nerve against Mawson as they swept through turn 1 to take a lead he would hold across the journey.
From there he was never headed, the race running green as he streaked to a 2.4s win that also sealed round honours ahead of Mawson.
"It feels incredible; I'm super stoked with that, really happy,": said Webster.
"Joey gave it to me on the start; I didn't get one of my grouse starts but it was alright.
"He gave it to me the best he could down to turn 1 and I knew it was on. But I held him off at turn 1 and nailed the rest of the race, and it was game over."
Mawson added: "First of all, congratulations to Cooper. He did a fantastic race. As for myself, I still collected solid points and got a podium, so still a positive weekend overall."
James Golding finished the final heat third, half a second behind Mawson and well clear of Garry Rogers Motorsport teammate Aaron Cameron.
Blake Purdie, who ran third in the early stages, slipped back to fifth as the race wore on ahead of Nic Carroll and Jordan Boys.
The S5000 Australian Drivers' Championship season continues at Winton on June 9-11.
