Wales had gone into the game as underdogs having never won on French soil and having won only two of their last 11 Six Nations outings.
But tries from Kate Williams and Gwen Crabb saw the visitors very much in the contest at half-time.
Lynn admits it was the French scores either side of half-time which proved decisive.
“I call those the championship minutes, but the girls felt really confident going in at half-time and the coaching staff too,” he said.
“We’ve got to take that as a positive because you’re coming out here in front of an amazing crowd, in an amazing stadium and we are competing with France.”
Lynn agreed that the final scoreline did not reflect the effort of his players.
“I totally agree. 42-12 we are better than that, but full credit to France, the way they played and opened it up, their offloading game is typical “jeu” and it’s lovely to see, but we are better than that.”
Wales will now go in search of their first win under Lynn when they host Ireland at Rodney Parade on Sunday, 20 April.
France, meanwhile, remain on course for a Grand Slam decider against defending champions England on the final day of the championship on Saturday, 26 April.
