The Parisian club has now won the prestigious cup on 14 different times.
Paris Saint-Germain required a dramatic equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders seemed to be coasting towards a straightforward triumph in the match between the French league champions and the French Cup holders after the French winger found the net in the opening stages.
However, Marseille fired twice late to take a shock lead. Initially, Mason Greenwood converted from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of fortune, the Portuguese striker snatched a vital leveler in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping crucial attempts from O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored with composure for PSG to seal a convincing penalty victory.
Now 14-time champions PSG, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this trophy for the twelfth time in the past 13 years.