Luka Modric's fifth-minute penalty at the Stade de France earned Zlatko Dalic's side a 1-0 win on Tuesday (AEST), with Croatia gaining a measure of revenge for its 2018 World Cup final defeat.
The loss means France can no longer finish top of Group A1, and as such prevents it from qualifying for the Nations League finals and retaining its crown.
France is not in action again now until September, when its objective will be avoiding a humiliating relegation from the Nations League's top tier.
They certainly have work to do on that front as they sit bottom of the group after four games, having only mustered two draws and a couple of defeats this month.
Deschamps seemed to blame fatigue for France's struggles but also accepted the players of most other teams will have been in a comparable condition physically.
Speaking at full-time, Deschamps said: "This month of June was very difficult in terms of results.
"We didn't have enough energy and strength against teams that had more than us. We weren't successful either. It was above all the freshness that was not there.
"There are always lessons to be learned with these results. Each match is rich in lessons.
"The succession of matches was very hard, we lost players from one match to another. No doubt that others nations were affected [by fatigue].
"[The players] will have to clear their heads and go back to their club and start again for this new season."
The defeat represented the first match since November 2020 in which France failed to score (23 games).