Pocock damaged the articular cartilage of his right knee during last Saturday's Bledisloe Cup defeat against New Zealand in Sydney.
He will now miss the rest of the Rugby Championship and his position on November's Spring Tour is also in doubt. Half-back Will Genia will take over as skipper.
Pocock's knee injury has opened the way for rookie Michael Hooper to take over the number seven jersey in Australia's return Bledisloe Cup match in New Zealand on Saturday.
It will be a day of firsts for Hooper - not only has he never played at Auckland's Eden Park, but he is set to make his starting debut against Richie McCaw, a player he has never come up against before.
Hooper has been paying attention to the way his opposite number at the All Blacks goes about his game.
"I think I've watched him (McCaw) more recently than I have over the past years - I've really been taking notice," Hooper said.
"Over the past few weeks, with the potential to come up against him, you start looking at the things he does. He's an outstanding player, someone who I think every open-side flanker in the world will take things from."
The Wallabies admit they were bullied at the breakdown by the All Blacks and Hooper said they will be looking to show more aggression in that area this weekend.
"The physicality is a step up and there are certain things the opposition do to make life difficult for you. So it's a different challenge, but I'm sure I'll speak to Pocock more about it," he said.
The Wallabies' chances of a rare away success in New Zealand were hit further when prop Sekope Kepu was ruled out of the Test at Eden Park with a knee injury.
The 26-year-old suffered a grade two strain to the medial ligament of his right knee during a training session in Sydney, the Wallabies said in a media release.
No replacement has been called up to the squad. Coach Robbie Deans is scheduled to name his team on Thursday.