Cooper ruptured his anterior cruciate ligament in the Rugby World Cup bronze medal match against Wales and was forced to sit out Australia's recent two-Test tour of the northern hemisphere.
James O'Connor stepped in at fly-half in his absence and received rave reviews after strong showings in both victories over the Barbarians and Wales.
Barnes was also among the star performers at inside centre, prompting suggestions his partnership with O'Connor was Australia's most potent playmaking combination.
But Barnes believes Cooper, who endured a disappointing World Cup campaign, will return from injury a far better player.
"At the end of the day you've got to understand that Quade's an outstanding player at this level," Barnes said.
"Last year he dominated, or earlier this year anyway. Obviously injury has cut him down, and I've been in the same place before as well.
"So he's going to have time off to get himself right and at the end of the day he should come back better than ever after the time off he's had."
Pressed on his own combination with the prodigious O'Connor, Barnes said: "It seemed to work alright, he did extremely well in his first outing there at Test level and the boys around him provided that help and the forwards provided that platform for him to be able to show what he can to do.
"Across the board there in Wales everybody played their part in that win and that was the handy thing about it.
"There weren't any individual (stars), it was more of a team thing and that's the exciting thing moving forward."