The Real Madrid number nine opened the scoring inside 10 minutes in Bergamo, and looked very lively, forcing La Dea goalkeeper Marco Carnesecchi into two fine saves either side of his goal.
However, shortly after the half-hour mark, Mbappe dropped to the turf and made the signal to the bench to come off.
Mbappe was then replaced by Rodrygo, but Vinicius Junior and Jude Bellingham did the business in the second half to get Carlo Ancelotti's side over the line with a narrow win in Northern Italy.
Mbappe update issued quickly post-match
The Real Madrid forward did not look in much pain when leaving the field, and was able to walk off unassisted, suggesting that the problem was not too serious.
Real Madrid TV have since clarified after the game that Mbappe was replaced because he simply felt discomfort in his hamstring, as opposed to any actual injury, and the medical staff opted to take no chances and recommended him to be subbed off as a precaution.
Ancelotti also said in his post-match press conference: "Kylian Mbappe's injury does not seem serious. It's an overload."
Mbappe will undergo tests tomorrow morning to discover the extent of the problem, and whether it will rule him out of the clash with Rayo Vallecano at the weekend.
Los Blancos could overtake Barcelona at the top of La Liga for a brief time at least if they win on Saturday night against their Madrid neighbours, before they jet off for the Intercontinental Cup in Qatar.
A change of format means that the Champions League winners now receive a bye straight into the final, which will take place in Lusail on December 18.
Real will then return to league action against Sevilla for the final time in 2024 on December 22, before a much-needed two-week break before the Copa del Rey and Spanish Super Cup in the new year.
Mbappe sets impressive feat in Atalanta win
Despite playing only 35 minutes, being forced off early, that did not stop Mbappe from having a huge influence on proceedings in Bergamo.
The early goal saw him become the second-youngest player to reach 50 Champions League goals, with only Lionel Messi hitting the feat at a younger age, doing so when he was 24 and 11 months, compared to Mbappe doing so at 25 and 11 months.
As far as legendary French strikers go, Mbappe has now matched Thierry Henry's Champions League tally, meaning all he has left to do is win the competition to equal the legacy of one of France's all-time greats.
Mbappe is just the ninth player to reach a half-century of goals in the competition's history, and he will now have his eyes set on catching up to Thomas Muller and Ruud van Nistelrooy, who currently sit in the mid-50s.
Written by
Andrew Delaney