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.
As the countdown continues for RWC2015, Tournament Chief Executive Debbie Jevans visited the Millennium Stadium to discuss preparations for the eight matches and reveal the positive news that 100,000 tickets for games at the home of Welsh rugby have sold in the last seven days.
Jason Harries is targeting a first win on the World Series circuit this season with Wales. The series returns to action this weekend in Dubai where Harries is part of a team hoping to build from its efforts in round one in October.
Wales skipper Jevon Groves says his side have addressed a few points from Gold Coast and aim to 'hit the ground running' in the next two rounds of the World Series, kicking off with this weekend in Dubai before heading off to South Africa next week.
Wales Sevens manager Steff Thomas is hopeful his side can build from a quarter-final spot in the opening round of the World Series in Australia when his side take part in the forthcoming double header in Dubai and South Africa.