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.
The last five years have been an emotional rollercoaster on and off the pitch for RGC1404. Promotion to the Principality Premiership was the culmination of five years of hard work and investment in North Wales. WRU TV caught up with prop Joe Simpson, who was one of the first intake of WRU North Wales Academy players in 2010.
Ebbw Vale captain Damien Hudd picked up the biggest accolade of the night at the 11th Principality Premiership Awards Evening held at Principality Stadium, after leading his side to the title for the first time.
Wales assistant coach Robin McBryde is predicting a tough battle against England on Sunday despite the fact they may not be considered to be at full strength. Players will be out to impress Eddie Jones which makes England a dangerous proposition, he says.
Wales U20 captain Tom Phillips and performance psychologist Dr Rich Neil explain why spending three days at Monmouth RFC has further strengthened the togetherness of the squad ahead of the #WorldRugbyU20s