It means Thomas will be in a race against time to be fit for the Blues first Heineken Cup clash away to Racing Metro on Friday November 11.
Williams made 52 appearances in Europe during his career, playing for Pontypridd, Bridgend and the Blues during that time.
He came off the bench at the Stade Vélodrome in 2010 as the Blues lifted their first European title with victory over Toulon but has failed to recover from a neck injury which was picked up in pre-season.
"Basically, the neck was damaged during the pre season friendly against Bath," he said.
"I damaged some more discs in the neck close to where I had the operation last year, which are now fused together."
"If I were to have the operation, it would be quite a big procedure and the doctors said that if I did come back playing, I would be opening myself up to maybe some permanent damage and there is no guarantee it would work."
"So it's too much of a risk, especially in the position that I play in the front row."
"His advice was to retire and so I'm hanging up my boots -
"It still hasn't sunk in, but the surgeon has made the choice for me."