Mbappe left out of France squad for Israel and Italy fixtures
Deschamps did not say whether Mbappe, who played with his club in the Champions League on Tuesday, was injured, arguing his choice was a "one-off decision" and that the player "wanted to come" and join the team.
Mbappe, who has been struggling for form after joining Real from Paris St Germain in the close season, missed two France games last month, against Israel and Belgium.
"I've had discussions with him, it is a decision that I took for this block of matches only," Deschamps told a press conference. "Kylian wanted to come."
France, who are second in Group A2 a point behind Italy after four games, take on Israel next Thursday at the Stade de France and travel to face the Italians on November 17th.