Zlatan Ibrahimovic continued his sensation run of form with the opening goal against the Greek club but the 80th minute, defender Manolas found the back of the net with a tap in.
But PSG's other towering striker Edinson Cavani netted a late winner after beating the trap before shooting past the keeper to win.
Goals and key events:
7' Ibrahimovic
80' Manolas
90' Cavani