The 24-year-old faces reconstructive surgery and will be out of action for at least six months.
The injury rules him out of all three Tests against Britain and Ireland's elite in Brisbane on June 22, Melbourne on June 29 and Sydney on July 6, as well as the remainder of the Super Rugby season and the Rugby Championship campaign.
"To hurt my knee so early in the season is obviously disappointing, particularly considering how well the team (the Brumbies) has been playing," Pocock tweeted.
"When I got here last year I got a good feel for the club's rehab programs and structures, so I know what I'm in for as far as getting my knee back to full strength.
"The medical staff have given me plenty of time to make a full recovery, so my focus has to turn to making that a reality."
Pocock limped out of the Brumbies' 35-6 thrashing of the Waratahs in Canberra after just 14 minutes of only his third competitive game for his new franchise.
His absence against the Lions will be a huge blow for Wallaby head coach Robbie Deans, who had been tipped to name Pocock as his captain for 2013.
Deans is expected to select Tahs youngster Michael Hooper as his replacement at the Suncorp Stadium in three-and-a-half months' time after he made a massive impression when Pockock sat out 10 straight Tests in 2012 with an earlier knee problem.
Hooper picked up three man-of-the-match accolades in his debut Rugby Championship campaign and was the standout player in the November win over England at Twickenham.
But Deans also has other strong options in the form of Reds flanker Liam Gill and new Brumbies signing George Smith.
Gill is being backed to become as good an openside as both Pocock and Hooper in future years, while Smith produced a superb display when replacing Pocock on Saturday.
The 32-year-old showed the class that earned him 110 Wallaby caps before his departure for France and then Japan and Deans may now attempt to persuade him to extend his initial 12-week contract in Canberra.