The attacker was left out of Saturday's Ligue 1 win over Lens because of the ailment. He then had to train separately from the PSG squad during the buildup to their second Champions League semifinal meeting with City.
He was named to the bench for Tuesday's clash, but ultimately didn't feature.
Mauro Icardi replaced Mbappe in Mauricio Pochettino's XI.
Manchester City went on to claim a 2-0 win on the night, giving them a 4-1 victory on aggregate and a place in the Champions League final.