The latest news is a bitter blow for Thomas after the versatile flanker missed all four autumn internationals and only returned to international colours for the Six Nations win over Italy last month.
The 26-year-old offers significant lineout options which had led to him being talked about as a possible Lions contender for the forthcoming series against the Springboks.
Instead, Thomas will be unavailable for the tour, as well as the Osprey's Heineken Cup quarter final in Munster and their Magners League run in.
"It's been a shocker of a season for myself in terms of injury," said Thomas.
"So I'm quite realistic that I need to get the rest in if I want to come back next season.
"I saw a specialist and he said the only way to cure it is to have at least three months' rest.
"Obviously I'm bitterly disappointed with that, but the time had come where I've had the problem so long."