Given the chance to lead the line in Olivier Giroud's absence, the Paris Saint-Germain star saw little of the ball before sustaining a seemingly minor injury in a tangle with Raul Castro.
Les Bleus boss Didier Deschamps will hope the young forward can recover in time for what is his team's toughest assignment in Group H, though the manager said after the match that the injury was "nothing serious".
Following the game against Turkey, France will travel to face Andorra three days later at the Estadi Nacional.
The World Cup champions began qualification for Euro 2020 with a pair of wins in March, a 4-1 victory over Moldova followed by a 4-0 shutout of Iceland.
Mbappe is coming off a stellar season with PSG, having won the Ligue 1 Player of the Year award and finished the campaign as the league's top scorer with 33 goals.
The forward's stellar performances have let to constant speculation over a move, with Real Madrid among the clubs linked.
Mbappe himself has fanned the flames of that exit talk, hinting at a move away from Parc des Princes last month.
"I come to a first or a second turning point in my career," Mbappe said after collecting the Ligue 1 Player of the year award.
"I discovered a lot of things here. I feel it's time to have more responsibility. I hope it may be Paris Saint-Germain, it will be with great pleasure, or it may be elsewhere for a new project, but I would like to say thank you."
Since joining PSG, Mbappe has won the league twice while also claiming a Coupe de France and a Coupe de la Ligue title.
On Sunday, France would go on to defeat Bolivia 2-0 in Nantes following goals from Thomas Lemar and Antoine Griezmann.