The 19-year-old, younger brother of Real Madrid star Kylian, was dismissed in the 56th minute, shortly after the Spanish side scored what proved to be the winning goal.
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Mbappe raised his arm into Natan's face as play was about to resume. Although the incident initially escaped the referee's attention, a VAR review resulted in a straight red card.
UEFA has now confirmed a three-game ban, ruling the France youth international out of Lille's trip to Arsenal on October 13 and subsequent home fixtures against Galatasaray and Bodo/Glimt.
The former Paris Saint-Germain academy player will be available again for Lille's Champions League encounter with Bayern Munich after serving his suspension in full.