The right winger underwent surgery on Monday and now faces a lengthy spell on the sidelines that will rule him out of the remainder of Ulster's league campaign, and the 2016 Six Nations with Ireland.
Injury has been a constant thorn in Bowe's side in recent seasons, with hand and knee injuries putting him on the sidelines for a large part of 2013 before a groin problem also kept him out of the Ulster side for the first half of 2014.
It comes as bad news for Neil Doak's side, who will also be without Ireland stars Iain Henderson and Jared Payne after they too were both injured during the World Cup.
Henderson needs an operation on his hand and is out for six weeks, while Payne had a fractured foot stabilised through surgery but it is not yet known how long he will be out of action.
A statement from Ulster Rugby said: "Tommy (Bowe) sustained posterior cruciate ligament and meniscal injuries to his right knee during the Rugby World Cup quarter final against Argentina.
"He had successful surgery to repair the damage yesterday and he will be ruled out for at least six months."
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