Pocock had a two-hour operation in Brisbane on Thursday night to repair the anterior cruciate ligament he ruptured in the Brumbies' 35-6 Super Rugby win over NSW last weekend.
It's a massive blow for both the 24-year-old and the Wallabies ahead of the British and Irish Lions series.
Pocock opted against gambling on the radical LARS surgery which could have had him back in the frame to play the three-Test Lions series, kicking off on June 22.
Regarded alongside All Blacks skipper Richie McCaw as the best No.7 in the world, Pocock is now an outside chance for Australia's November tour of Europe.
"I'm pleased to have the surgery out of the way," Pocock said in a statement.
"Now I need to rest up and get myself ready to start the rehabilitation process.
"The key thing is that I'm patient and don't try to rush back.
"If that means season over, in terms of playing any more rugby this year, then so be it.
"Once I get into the rehabilitation, we'll see how it goes."
The reconstruction, overseen by noted surgeon Peter Myers, was completed late Thursday night.
NSW Waratahs flanker Michael Hooper, who started in Pocock's absence for much of last year, and Queensland's in-form Liam Gill are vying for the Wallabies No.7 jersey while Brumbies veteran George Smith is currently deemed ineligible due to his contract with Japanese club Suntory.