A try from replacement Brad Scannell, three penalties from outside-half Corey Evans and a long-range penalty from full-back Jac Lewis were enough to edge out the Mid Glamorgan club.
A weary Thomas, whose assistant coach with Morriston is former Wales outside-half Arwel Thomas, will return to the Turkish resort of Antalya tomorrow.
He said: “We had gone for a week but I had to come back for this. They (team) just had to win after I left the family behind.”
Thomas will spend barely 24 hours in Wales before re-joining a 28-strong party of Morriston U12 players and their families in Turkey for the remainder of a week-long break.
He will jet out with a big smile on his face, saying: “It was a brutal game between two very physical sides. Aberdare were the third Central team we have played in this competition and they have all been tough matches. They had some strong ball-carriers.”
Thomas was delighted that, out of the 23 Morriston players on duty, he had coached 17 of them at youth level.
“They are all Morriston born and bred and have got a really good bond after coming through the ranks together,” he said.
Thomas revealed he had given try-scorer Scannell a rollicking just before he got the winner.
“I sent on a message giving him a rocket about being switched on. Two minutes later he scores,” added Thomas.
Former Wales play-maker Arwel Thomas said: “I’m happy for the boys, they deserve it for what they have put in.”