His opposite number Rhys Patchell did his best to keep the Blues within reach, but despite his two penalties they fell to their sixth defeat in seven games.
The Scarlets were dominating much of the early possession - they almost snatched a try from a chargedown after two minutes - but eventually settled for three points from the boot of Thomas on four minutes.
Thomas, whose last kick in the RaboDirect PRO12 got them a losing bonus point against Ulster, added another penalty on ten minutes after a powerful scrum from the visitors forced the Blues into conceding a penalty.
The hosts got themselves on the scoresheet five minutes later though, in their first stint in the Scarlets' territory they won a penalty and Patchell converted.
Set-pieces were proving scrappy for both sides, in particular lineouts which were thrown long and wayward on too many occasions during the middle of the half.
With chances few and far between Thomas' kick on the half hour, arguably his easiest of the night, took on extra significance but was skewed wide.
An excellent lineout drive from Cardiff moments later though almost brought its rewards, but when the ball came loose Patchell failed to release quickly enough to take advantage of the numbers out wide - and the fly-half missed the resulting penalty.
Thomas, perhaps smarting from his earlier miss, made amends by kicking his next attempt a minute before the break which saw the Scarlets take a 9-3 lead at half-time.
The visitors came out strongest after the interval but a deliberate spell of pressure, lasting 16 phases, fizzled out to nothing but the Blues defence was being given a stern examination.
At the other end Patchell kicked the Blues within three points with his second penalty on 57 minutes before Thomas missed his attempted penalty ten minutes later.
Thomas then had the chance to set Liam Williams free with five minutes to go, but his pass was deemed forward and the full-back's try was ruled out.
And despite coming up short with a penalty in the final minute, Thomas and the Scarlets held on for their fifth victory in six RaboDirect PRO12 games.
|Cardiff Blues Score Card|
|Scarlets Score Card|