Wales made a dream start with former Great Britain rugby league star Iestyn Harris making the initial break down the left before he was hauled down by a scrambling French defence.
But the ball was quickly recycled to the right flank where France were over-stretched, allowing Thomas to take the final pass before sprinting in at the corner.
Stephen Jones missed the conversion but he almost set up the next try just two minutes later when his punt down field bounced over the line with the on-rushing Craig Morgan on hand to touch down only for the video official to rule no try.
France then took charge and they could not be denied in the 27th minute when centre Damien Traille fed Castaignede who crossed under the posts, with Dmitri Yachvili adding an easy conversion.
The Biarritz scrum-half then slotted the first penalty of the afternoon to reward the home side's continued dominance, and Jones compounded his side's misery by missing a very kickable three points shortly after.
The second half began with Yachvili kicking a penalty and France's lead was extended in the 51st minute when substitute Clerc dived over the line after a quick break.
The near-touchline conversion was booted by Yachvili to effectively put the game out of Wales' reach. He then kicked his third penalty before Michalak crossed in the 66th minute.