The 19-year-old forward had to be replaced after landing awkwardly following a collision with visiting goalkeeper Martin Campana.
It continued a worrying night for PSG coach Thomas Tuchel, who had already seen Neymar hobble out of Brazil's match against Cameroon in Milton Keynes barely an hour before.
The World Cup winner looked in some pain as physios examined his shoulder, although he initially played on. Unfortunately, minutes later he looked to the bench, still in obvious pain, and made it clear he would need to be substituted.
The French champions host Liverpool in a crucial Champions League game on November 28.