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 reached their first semi-final since 2013 in the opening round of this season's HSBC World Rugby Sevens Series in Dubai. WRU TV's Graeme Gillespie recaps on what proved to be an eventful tournament
Wales and Ospreys back row James King, who came through the North Wales age grade system, nominated North Wales Regional Community Rugby Manager Marc Roberts, in the WRU's 'Diolch' initiative where squad players thanked those who played a part in their rise to the top.
Beating Merthyr has boosted Carmarthen Quins hopes of reaching a top eight spot in the Principality Premiership. Quins captain Haydn Pugh is delighted with his team's progress and is determined that everyone from the Under 6s through to the senior team, enjoys the ride.
When the Wales squad were asked to nominate individuals who played a big part in their early playing days, Wales and Dragons full back and wing Hallam Amos thought of his former Monmouth School rugby coach John Bevan.
Sam Cross and Luke Treharne have been named as co-captains of the Wales Sevens side as head coach Gareth Williams names his 12-man squad to play in the first leg of the HSBC World Series in Dubai next weekend.
Bedwas head coach Steve Law and players Nicky Griffiths and Alun Rees extol the virtues of the close knit club as they prepare to host third place RGC 1404 - who are one place head of them on the Principality Premiership points table - on Saturday.
Many of the Wales squad have said Diolch (thank you) to someone who played an important part in their early playing days by nominating them to be invited to the Wales v South Africa match. One person, Gowerton Comprehensive geography teacher Mr Dean Mason was nominated by two of his former pupils, Dan Biggar and Sam Davies.
The second WRU disability rugby pilot has been delivered, this time in Caerphilly schools, culminating in a festival at the Caerphilly Centre of Sporting Excellence, Ystrad Mynach tomorrow. Plans are in place to set up a Disability Rugby Club in Newbridge to provide long-term playing opportunities.
WRU TV: Hear from inside the Wales camp as Neil Jenkins discusses this weekend's clash with South Africa and how the squad are looking to put in a strong performance to round of the 2016 Under Armour Series