The usually prolific Mbappe has not been at his best for France during the Euros, scoring once from the penalty spot against Poland but otherwise failing to convert chances and looking uncomfortable in a mask after breaking his nose in the first game.
Against Portugal in the quarter-final on Friday night, he spent time on the ground and briefly removed his mask after a hard hit from the ball on the side of his face, before later asking to be taken off and missing the shootout.
"Yes, he's always very honest with me and the team, when he feels he doesn't have the capacity to accelerate... He's not at his top form ... he felt very tired indeed," Deschamps said, referring to muscle fatigue and the nose issue.
"I saw him struggling during the first period of extra time. It was pointless (to leave him on). Kylian has always been honest with me and the group, so it was only natural to bring in some new blood."
In his absence, Mbappe's teammates did him proud, scoring a perfect five penalties to beat Portugal 5-3.
