Thomas, Wales’ record international try-scorer, was stretched off midway through the second half.
He appeared to be suffering from an ankle ligament injury, casting major doubt over his Wales tour prospects in Argentina and South Africa next month.
Thomas is due to sign on the dotted line for twice European champions Toulouse today after agreeing a two-year contract worth around £250,000.
His departure took the gloss off a sound Welsh display that featured tries for Thomas, Rhys Williams, Dwayne Peel, Gavin Henson, Hal Luscombe and Ceri Sweeney, while fly-half Sweeney added a further 12 points from the boot.
It was the first time that the Barbarians had failed to score in a fixture since Newport beat them 30-0, 26 years ago.
: G. Thomas, R. Williams, Parker, Henson, S. Williams, Sweeney, Peel, D. Jones, Davies, A. Jones, Cockbain, Llewellyn, Charvis, Forster, Owen. Replacements: Luscombe for G. Thomas (65).
: Tries: Sweeney, G. Thomas, R. Williams, Peel, Henson, Luscombe. Cons: Sweeney 3. Pens: Sweeney 2.
: Barbarians: Reihana, James, Traille, Grey, Paulse, Burke, N. de Kock, le Roux, Sexton, Bands, Mika, Connors, Magne, Vos, E. Miller. Replacements: Leonard for Bands (55).