Proctor looked uncomfortable on Friday as he left the field after being injured in a clear-out at a ruck and is the second player to head home injured after hooker George Bell sustained a calf injury in training.
"Scans have revealed Billy Proctor has a shoulder blade fracture," a statement from the All Blacks on Sunday.
"This will not require surgery but will take approximately 10 to 12 weeks of recovery, meaning Billy has been ruled out of the remainder of the tour."
There has been no word of a replacement as yet, but it could open the door for fly-half Richie Mo'unga to return to the squad.
New Zealand have three more fixtures against South African franchise teams, starting on Tuesday against the Sharks in Durban.
They also take on the world champion Springboks in four tests starting on August 22, the last of which is in Baltimore in the United States.
"Billy unfortunately is going home. He'll go home on Thursday. He's got a fractured shoulder blade. A big vertical fracture through that," Rennie said at a team press conference.
"I'm devastated for him. He'll head home on the same plane as George Bell. We will [call in a replacement] but we're going through that process."
