Mbappe received lengthy treatment but was eventually substituted after his right ankle was caught by a clumsy Perrin challenge that resulted in a red card for the centre-back in his final game for St Etienne.
The referee had only shown a yellow card initially, but it was upgraded after a VAR review.
Mbappe went off crying and was replaced by Pablo Sarabia but the greater concern for PSG will be the severity of his injury ahead of next month's Champions League quarter-final against Atalanta in Lisbon.
PSG also face Lyon in the French League Cup final next Friday before resuming their European campaign in a reworked tournament at the Estadio da Luz on August 12.
In the second half, Mbappe emerged from the tunnel on crutches. It is not good news for the French outfit.