The flanker damaged his articular cartilage in his right knee during the 27-19 loss to the All Blacks in the opening Rugby Championship encounter.
Pocock, 26, will now have keyhole surgery on Tuesday - ruling him out of Saturday's rematch at Eden Park.
"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," Australia coach Robbie Deans said.
No timescale has been placed on Pocock's possible return.
Will Genia, who captained Australia against the USA at the World Cup, will replace Pocock as skipper - while Michael Hooper and Liam Gill are vying for a spot in the back-row.