The flanker suffered damage to the articular cartilage in his right knee in the first half of Saturday’s 27-19 loss to New Zealand in the Rugby Championship opener in Sydney.
While Pocock played through the pain to complete the match, scans confirmed he will need an operation.
“He will undergo keyhole surgery in Sydney tomorrow (Tuesday), with a decision on the time period of his rehabilitation to be determined following the procedure,” the Australian Rugby Union said.
Vice captain Will Genia is set to take the skipper’s armband for the Eden Park showdown which doubles as the second of three Tests to decide the Bledisloe Cup.
The Wallabies must win in Auckland for the first time since 1986 to prevent the All Blacks from holding the title for a 10th consecutive year.
Pocock said he was not sure how long he would be sidelined.
“He (the surgeon) said he wanted to avoid putting a timeline on it till after he actually got in there to have a look,” Pocock told reporters.
Coach Robbie Deans said it was unfortunate for Pocock and the team, which is already without first-choice captain James Horwill, who had surgery on his hamstring in June and will be out for months.
“It’s disappointing for him and obviously not what we were seeking, but that’s the way it is and it’s part of the game,” Deans said of Pocock.
Michael Hooper, who has played for Australia three times before, is expected to replace Pocock, although the uncapped Liam Gill is also in contention.
Deans said he had confidence in Genia, who has captained Australia once before, against the United States at last year’s World Cup, to lead from the front in Saturday’s must-win encounter.
“He responds to that sort of responsibility and I’ve got no doubt he will do so here,” he said.
While Pocock is an enormous loss, Deans also has a headache over whether to retain fullback Kurtley Beale after an error-strewn performance in Sydney, a defeat characterised by basic handling errors and missed one-on-one tackles.
If he drops him he may have no choice but to recall the unpredictable and controversial Quade Cooper, who is on the comeback trail from knee surgery.
Cooper fell short of expectations at the World Cup and he would receive a hostile reception at Eden Park after being accused of cheap shots on All Blacks captain Richie McCaw last year.
But he could help reignite the Wallaby attack and give them more kicking options.
“Quade will be considered, no doubt about that,” said Deans.
“We’ve got to try to find ways to win, which isn’t straightforward.”