In his first Super Rugby match in Brisbane since his acrimonious departure from the Reds, Cooper set up two tries and scored 12 points off the boot in a 32-12 win at Suncorp Stadium on Saturday.
After the match Cooper revealed while he was pleased to get the win, it had been a tough night playing against his "brothers" in the Reds line-up.
"It wasn't the boys that didn't want me, and the boys are the ones that we're playing against," Cooper told Fox Sports.
"Obviously I don't want to see them go down. I want to get the win when we play against them but I'm always supporting them.
"I want this franchise to do well and it's a little bit sad to see when they're struggling a little bit, on and off the field."
Cooper got the scoring under way with a second-minute penalty but despite the Rebels dominating territory and possession the scores were locked 6-6 nearing halftime.
It was Cooper's pinpoint cross-field kick which set up the first try on the stroke of halftime, with Rebels winger Jack Maddocks out-jumping Hamish Stewart to give the Rebels an 11-6 advantage.
After the break, the Rebels capitalised on an early Reds penalty to again hold the territory advantage with Anaru Rangi peeling off the back of a maul to score.
Another Reds error, this time a dropped ball, led to a third try for the Rebels in the 47th minute.
Cooper pounced on the loose ball near the halfway line, twice soccering through before Maddocks won the race to extend the lead to 25-6.
The home team thought they'd got one back when Brandon Paenga-Amosa crashed over from close range but a TMO review after the try had been awarded detected a knock-on by Reds halfback Tate McDermott.
The Reds did eventually get a try when Taniela Tupou scored late in the game, but the scoring wasn't done, Rebels substitute Rob Leota capping a 15-phase move to score in the final minute and claim a bonus point.
Fittingly Cooper ended the action with a conversion before immediately embracing Reds captain Samu Kerevi.
Rebels coach David Wessels praised the efforts of his No 10 and fellow ex-Reds player Will Genia in helping secure the victory.
"They were instrumental tonight in controlling the game and the tempo of the game," Wessels said.
"This is a special place for them."
Reds coach Brad Thorn said his team simply never got going in the match, a situation that was created by their opponents' good play.
"Most of the first half we were sort of parked down in our own half and when you give teams those opportunities, sooner or later they're going to make you pay for them aren't they?" Thorn said.
"They did well considering they came back from Africa - it's always a tough game - and they did what they had to do to get the win. In the end they won really well."
Victory lifts the Rebels to the top of the Australian conference after the Waratahs' shock loss to the Sunwolves on Friday.
Genia, who played with an infected cheek, will spend the night in hospital undergoing a course of antibiotics but should be fit to face the Sunwolves in Melbourne next week while Reds youngster Angus Scott-Young will have to pass concussion protocols after failing a HIA in the first half.