Starting from pole, Clemente made a clean start to lead the field through the turns 1/2 complex.
Honda's Tony D'Alberto made a fast start from the second row and tried to challenge Hyundai pair Josh Buchan and Bailey Sweeny, however ended up wide at the first two corners before copping a hit from Peugeot driver Jordan Cox at turn 3.
That sent the factory-supported Honda back to seventh.
As Clemente controlled proceedings at the front, the two Hyundais started to squabble over second place. On lap 3 Sweeney went around the outside of Buchan to grab second into turn 1, the duo then continuing to battle across the lap.
Eventually they slowed each other up, allowing Honda-shod Zac Soutar to squeeze in between them at the last corner.
That freed series leader Sweeny up to hunt down Clemente, who had shot into a lead of almost three seconds.
Sweeny made a good job of it, working to within a second of Clemente as the race counted down into the final five laps.
But that was as close as he could get, Clemente with enough up his sleeve to secure a second career TCR Australia win.
"It's been a pretty awesome weekend so far," said Clemente.
"It's an awesome car, the Cupra is really good to drive. It requires a completely different driving style but I think we're getting used to that, two rounds in.
"It's the start of something that hopefully ends up pretty good.
"[Sweeny's Hyundai] is quick, credit to Bailey and the team, he's driving it like a weapon. I got a decent start and I thought I could manage, but he came in really hot and I was giving it everything.
"It's probably going to be a good race tomorrow as well."
Zoutar came home third in his latest-spec Audi ahead of Buchan and Cox.
Reigning champion D'Alberto only improved to sixth, followed by Ben Bargwanna (Peugeot) and Lachlan Mineef (Audi).
TCR Australia debutant Clay Richards (Audi) and BTCC race winner Tim Oliphant (Alfa Romeo) were ninth and 10th, which means they'll share the front row for the partially-reverse grid race tomorrow.
