PSG has now secured the prestigious cup on fourteen different occasions.
The Parisian giants required a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be coasting towards a comfortable win in the match between the French league winners and the French Cup winners after Ousmane Dembele found the net in the opening stages.
Yet, Marseille struck twice in the closing moments to take a shock lead. Initially, Mason Greenwood scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a vital equaliser in the dying moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial attempts from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and the young talent all scored with composure for Paris Saint-Germain to seal a convincing penalty victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the last thirteen seasons.
