The 24-year-old suffered the problem during his side's defeat to Saracens in the Aviva Premiership last month.
He has now been told by doctors to rest until the summer.
An official Quins statement read: "Following further scans and guidance from specialists over the past four weeks, George has been advised not to play again this season.
"Instead he will undertake a programme of treatment that aims to have him fit to return to action for the 2014-15 season."
Lowe signed his first professional contract with Harlequins in 2009 after graduating from the club's youth academy.