Kante was named in the French squad for the previous international break but missed out through injury, included only as an unused substitute against Bosnia-Herzegovina.
The Chelsea man has not played for his country since Euro 2020 and will not now be involved against Belgium in the Nations League semi-final, nor in either the final or third-place play-off after that.
Kante was missing from Chelsea's 1-0 defeat at Juventus on Thursday (AEST) due to testing positive for COVID-19.
France coach Deschamps acknowledges Kante would have been cleared in time for the second Nations League Finals match on 11 October, but he doubts the midfielder would be in any condition to play to the best of his ability.
"It is 10 days since Monday, so you calculate," Deschamps said. "There was always the assumption that he would be there for the second game, but after 10 days without training, knowing that he was injured recently...
"I would prefer him to be there, but I also prefer him 100 per cent. Let him take advantage of this period to regain his physical freshness."
There is also no Kingsley Coman, who has been restricted to just eight minutes since the previous international break, or Thomas Lemar, as he battles a hamstring issue.
Steve Mandanda has been dropped after losing out to Pau Lopez in the Marseille goal, while Olivier Giroud's recent return for Milan is not enough for a recall – a "sporting choice", Deschamps explained, after other forwards impressed last time.
But the defence now looks a lot healthier, as Bayern Munich men Benjamin Pavard and Lucas Hernandez are able to rejoin the squad, as does team-mate Dayot Upamecano, who had to pull out last time. Deschamps listed Hernandez's brother Theo as a midfielder.
Crucially, the calf injury that kept Kylian Mbappe out of France's most recent games has subsided, meaning Deschamps must again attempt to strike a balance in attack, where Antoine Griezmann and Karim Benzema excelled in the Paris Saint-Germain forward's absence.
Griezmann, who has Deschamps' backing after a tricky start to his second stint at Atletico Madrid, scored twice against Finland – the first assisted by Benzema – as Les Bleus bounced back from draws with Ukraine and Bosnia-Herzegovina.
"What happened is in the past," Deschamps added. "There is a title to play for. We have a semi-final to play against one of the best teams in Europe and the world, if not the best.
"We have given everything to qualify for the Finals. Now, we are there. We keep the same state of mind; we want to go for the title."
Benoit Costil (Bordeaux), Hugo Lloris (Tottenham), Mike Maignan (Milan); Leo Dubois (Lyon), Lucas Digne (Everton), Lucas Hernandez (Bayern Munich), Presnel Kimpembe (Paris Saint-Germain), Jules Kounde (Sevilla), Benjamin Pavard (Bayern Munich), Dayot Upamecano (Bayern Munich), Raphael Varane (Manchester United); Matteo Guendouzi (Marseille), Theo Hernandez (Milan), Paul Pogba (Manchester United), Adrien Rabiot (Juventus), Aurelien Tchouameni (Monaco), Jordan Veretout (Roma); Wissam Ben Yedder (Monaco), Karim Benzema (Real Madrid), Moussa Diaby (Bayer Leverkusen), Antoine Griezmann (Barcelona), Anthony Martial (Manchester United), Kylian Mbappe (Paris Saint-Germain).