The captain received treatment on his knee immediately after the goal and briefly returned to the pitch but went down again about a minute later and was unable to continue.
"Unfortunately, it doesn't look good. I think he'll have to go back," Zidane said of Mbappe.
"We're not going to take any risks. He has swelling in the knee. It's not encouraging, so we're not going to take any risks."
Though under incessant pressure Turkey were able to cling on until the half-time whistle as Michael Olise's goal-bound effort was palmed away by Ugurcan Cakir before Adrien Rabiot's subsequent attempt sailed over the bar.
Turkey loomed large in the second half, and were left to rue squandering a glut of chances when Mbappe came to the fore in the 54th minute to give his side the advantage.
Found by Olise, the Real Madrid star took aim at the inside of the near post to claim his 67th international goal and leave Turkey lagging behind.
Left clutching at his knee, the 27-year-old was soon replaced by Desire Doue, who quickly drew a sharp save from Cakir, with the French Federation later saying Mbappe was returning to Madrid.
Turkey began to apply plenty of pressure in the hunt for an equaliser but it did not appear and instead Turkey were weakened by the dismissal of Cakir due to a handball outside his area.
Italy were defeated 2-0 by Belgium in Roberto Mancini's first match since returning as manager with the Azzurri having failed to qualify for three successive World Cups.
Mika Godts found the back of the net in the 20th minute and Dodi Lukebakio scored an excellent second midway through the second half.
Elsewhere, Liverpool striker Alexander Isak and Arsenal's Viktor Gyokeres both scored as Sweden defeated Romania 2-1 and Montenegro defeated Cyprus 2-1 as Nikola Krstovic's penalty and a Milutin Osmajic strike nullified Marcus Edwards' strike.
Ukraine came out on top against Hungary, with Danylo Sikan scoring the only goal of the game in the 42nd minute before the winning side were reduced to 10 men in stoppage time when Oleksandr Nazarenko was dismissed.
Pierce Charles saved Khvicha Kvaratskhelia's penalty before brother Shea scored a stoppage-time winner as Northern Ireland beat Georgia 1-0.
Armenia won 2-0 against Latvia while Poland and Bosnia and Herzegovina could not be split after a goalless draw.
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