PSG has now secured the prestigious cup on 14 separate occasions.
The Parisian giants needed a dramatic equaliser 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 seemed to be coasting towards a comfortable win in the showdown featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele opened the scoring early on.
Yet, Marseille struck twice late to take a shock advantage. First, Mason Greenwood scored from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a crucial leveler in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and the young talent all scored successfully for PSG to seal a convincing penalty victory.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now won this trophy for the 12th time in the past 13 years.