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.
Welsh players and management joined Deputy Minister for Sport Ken Skates at the Pierhead Building, Cardiff Bay earlier this week to reveal the Union's pioneering school-club hub initiative has been so successful the project will now almost double the scale of the original project.
The Scarlets, Newport Gwent Dragons, Cardiff Blues and the Ospreys look ahead to Judgement Day III which sees the Blues take on the Ospreys (2.30) and the Dragons tackle the Scarlets (4.45pm) at the Millennium Stadium tomorrow afternoon.
Ystradgynlais and Ynysddu played out a titanic struggle at Taffs Well in the SSE SWALEC Bowl semi-final. At the end of the game neither team could be separated after a 15-15 stalemate but Ystradgynlais go through on try count.
Blues strike first in JD III battle - Newport Gwent Dragons lock Andrew Coombs, WRU referee Dylan Llyr Jones and Cardiff Blues hooker Matthew Rees decide dressing room allocations for Judgement Day III
Wales Under 18 captain Calum Haggett has received a conditional offer to read Biomedical Science at St Anne's College, Oxford. WRU chairman Gareth Davies went to meet Calum and Coleg y Cymoedd Principal Judith Evans to wish him luck in his exams and pass on some of his personal experience.
Dodgy tattoos, carthorses, Avatar and soft chins are revealed by Wales Sevens players Tom Williams and Sam Cross as they profile the Wales Sevens squad taking part in Hong Kong this weekend in the latest round of the HSBC Sevens World Series.