"The team are devastated at Mike's decision," said Thomas.
"I respect him as a man and as a coach, he is a brilliant coach and a brilliant person.
"He played a vital part in the Grand Slam last year and we all now support him and his decision and wish him well in whatever he decides to do in the future."
Backs coach Scott Johnson has taken over at the helm for Wales for the remainder of the RBS 6 Nations Championship.
And former international hooker Robin Mcbryde - now a WRU national skills coach - has joined the coaching team to look after the forwards and work alongside existing defence coach Clive Griffiths.
"As for Scott Johnson, everyone knows what Scott means to the players," added Thomas.
"He has been with us for a long time now, the players know what he expects of them and there is nothing new in that respect.
"Scott has been with us through many ups and downs and we may be in for a tough time now but, with him in charge, we feel we can come through it.
"Mike felt 100% that we should play with Welsh pride and passion and if Jonno is in charge, I know we will carry on playing that Welsh way.
"Words are easy, but we want to put those words into action and go out on a high in this Championship and repay Mike for everything he has done for us."