Thomas, who had filled in during Nick Robinson's absence, will miss at least three weeks after damaging the AC-joint in his right shoulder during last weekend's defeat to Leinster.
It is yet another blow for the Blues who are already down to a skeleton team amid a catalogue of injuries and will leave coach Dai Young with third-choice fly-half Nick MacLeod for Monday's local derby against Newport Gwent Dragons at Rodney Parade.
Thomas said: "It couldn't have come a worst time, I'm gutted. I'd had a run of games in the starting team and there are some crucial fixtures coming up. This is going to be a very frustrating Christmas."
The Blues will also be without centre Jon Bryant, who made his debut for the club on Saturday, under the conditions of his move from the Dragons last week. However Tristan Davies made his return from a hand injury against Leinster and looks set to start.
Wales 7s Manager Steff Thomas believes Luke Treharne has all the attriubutes to be a top class captain. WRU TV's Graeme Gillespie hears his reasons why as the squad prepare for the opening two legs of the new World Series in Dubai and South Africa.
The British & Irish Cup kicks off this weekend with the four Regional Premiership Select XVs flying the flag for Wales. Welsh
Sat 14 Nov: Blues Premiership Select v Nottingham (2.30) & Connacht Eagles v Dragons (2.30)
Sun 15 Nov: Yorkshire Carnegie v Ospreys Premiership Select (1.30) & Scarlets v Bedford Blues (3.00)
The Welsh Rugby Union is forming a new Youth Board with a brief to help keep more young people involved in the game during their late teenage years and beyond. The first task of the fifteen strong Board will be to analyse and consider the issues which lead to a number of youngsters drifting away from the sport between the ages of 16 and 21. To apply visit www.wru.wales/youthboard
The Foster's Challenge Cup will involve the 12 Principality Premiership sides and will run during European and British & Irish Cup weeks, providing vital fixtures for the participating clubs and an opportunity for upcoming players to step up to semi-professional rugby and make a claim for starting places within the Premiership squads.
Eighty schools and colleges in Wales now have a full time rugby officer as part of the WRU's school club hub scheme. All of the school club hub officers recently gathered at the National Centre of Excellence for various workshops.
With Liam Williams forced out of the World Cup through injury, lock Luke Charteris and Skills Coach Neil Jenkins say they have to put yesterday's defeat behind them as Wales now look ahead to another physical encounter against South Africa in the quarter-finals of the Rugby World Cup.
WRU Consultant Head of Physical Performance Paul Stridgeon praises the Physical Performance department for their work and dedication as he addresses the media ahead of Wales' Pool A clash against Australia
Twelve young people have been selected to follow a one year WRU Coach Core apprenticeship programme. Coach Core was set up by the Royal Foundation of the Duke and Duchess of Cambridge and Prince Harry as part of the Olympics legacy in 2012 and the Duke of Cambridge was on hand to meet the apprentices on their first day in the job. The programme has been funded by the Hunter Foundation.