The Parisian club has now claimed the prestigious cup on 14 different times.
The Parisian giants required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be sailing towards a straightforward triumph in the showdown featuring the French league champions and the French Cup winners after the French winger opened the net in the opening stages.
Yet, Marseille struck twice late to seize a surprise advantage. First, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of fortune, the Portuguese striker snatched a crucial equaliser in the final seconds to send the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing shootout victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the 12th time in the past 13 years.