The flanker suffered a knee injury in Saturday's 27-19 loss to the All Blacks.
He struggled through the match but scans have now revealed Pocock damaged articular cartilage and requires surgery.
"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," said a Australian Rugby Union statement.
Vice captain Will Genia is set to lead the Wallabies at Eden Park in Pocock's absence
The Lions' next opponents have not won in Auckland since 1986 but need to end their losing streak to prevent the All Blacks hanging onto the title for the tenth straight year.
"It's disappointing for him (Pocock) and obviously not what we were seeking, but that's the way it is and it's part of the game," said Wallabies head coach Robbie Deans.
"Will responds to that sort of responsibility and I've got no doubt he will do so here."
Deans is also considering a recall for maverick play-maker Quade Cooper.
The Queensland Reds star missed much of the season due to a knee injury and was not considered for the first Test. But Deans is desperate to reignite the Wallabies' miss-firing backline.
"Quade will be considered, no doubt about that," added Deans. "We've got to try to find ways to win, which isn't straightforward."