The Parisian club has now won the prestigious cup on fourteen separate occasions.
The Parisian giants required a stoppage-time leveler followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The European champions appeared to be coasting towards a straightforward win in the showdown between the French league winners and the French Cup holders after Ousmane Dembele opened the net early on.
However, Marseille struck twice late to take a shock advantage. First, Mason Greenwood scored from the spot-kick, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a crucial equaliser in the final moments to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to complete a convincing penalty victory.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now won this trophy for the 12th time in the last thirteen seasons.