The forward missed the world champions' 2-1 win over Ivory Coast in Marseille when Olivier Giroud netted his 47th international goal, which put the AC Milan striker four shy of Thierry Henry's all-time France scoring record.
"He is much better, he will be there on Tuesday," Deschamps told French TV channel TF1.
He did not specify whether Mbappe would start the game.
South Africa, meanwhile, played to a 0-0 draw against Guinea in their friendly on Friday. Bafana Bafana are long out of contention for World Cup qualification.