Kounde was replaced by William Saliba in the 23rd minute, while Maignan played until halftime before being substituted for Alphonse Areola in the second half at Stade de France.
"Jules had a hamstring problem and Mike (had) a calf muscle problem. They will not be available for Sunday's game in Denmark," Deschamps said.
More than a dozen France players are injured, with striker Karim Benzema, keeper Hugo Lloris and midfielder Paul Pogba among the key absentees.
"The players are under a lot of pressure with the succession of matches. There are also psychological demands," Deschamps added.
"We are losing two more players ... Two more is a lot. In two months' time, if I can have none, that would be perfect."
France, who are third in their Nations League group with five points from as many games, begin the defence of their World Cup title in Qatar against Australia on November 22.