But Simon Davies' Welsh side hit back immediately after half-time with a try for replacement no 8 Daniel Baker and outside half Diggy Bird adding a conversion and a penalty to his first half goal, they sneaked ahead with five minutes to go and held on for the home nations bragging rights.
There were performances to note for Ospreys wing Eli Walker and Blues North openside flanker Thomas Young, son of Blues head coach Dai, who produced a good all-round performance, particularly in the second half.
Wales Under 16 recorded a second win in the Four Nations tournament with a stunning 17-16 victory over hosts France.
Wales and England have taken under 16 sides to the tournament while France and Italy are fielding under 17 teams, but Simon Davies' Welsh side did not let the age difference stop them, despite again trailing 16-3 at half-time.
The match followed a similar pattern to Wales' opening game, against England. France scored two early tries and added two penalty goals in the first half, while Wales were only able to respond with a penalty from Diggy Bird. However, after conceding the early scores, they built in momentum and came out after the break with all guns blazing. Centre and captain Sam Campbell (Blues North) nipped in for a try straight after the restart with Diggy Bird's conversion putting them within a score of the French.
For the remainder of the second half, the side displayed an immense collective effort, especially while down to 14 men for 10 minutes due to a yellow card for Campbell. They held on heroically and were rewarded with a try for Eli Walker with three minutes to go. The wing sprinted 75 metres to score under the posts, outside half Bird adding the extras to sneak a remarkable victory.
Team manager Darryl Hill said, "After holding on to beat England on Thursday, the boys again put in a tremendous team performance today and fully deserve to come away with the spoils. They never gave up and displayed 100% commitment from the first to the 80th minute. We play Italy Under 17 in Lyon on Wednesday and we're hoping to finish the tournament on a high with another victory."
Wales Under 16 squad:
Tom Prydie (Ospreys), Harley Thomson (Blues North), Owen Williams (Blues North), Eli Walker (Ospreys), George North (Scarlets), Dale Ford (Scarlets), Sam Campbell (capt, Blues North), Luke Williams (Scarlets), David Bird (Blues South), Joseff Griffin (Blues North), Aled Davies (Scarlets), Ryan Jones (Ospreys), Lewis Smout (Blues North), Tarian Emmanuel (Blues North), James Cromwell (Scarlets), Carl Williams (Blues North), Owen Davies (Blues North), Samson Lee (Scarlets), Luke Hamilton (vice-capt, Scarlets), Macauley Cook (Blues North), Rhydian Wilson (Dragons), Thomas Young (Blues North), David Barry (Blues North), Gareth Evans (Dragons), Kirby Perego-Myhill (Scarlets), Daniel Baker (Ospreys)