The Parisian club has now won the prestigious cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be coasting towards a comfortable win in the showdown featuring the French league champions and the Coupe de France winners after Ousmane Dembele found the net in the opening stages.
Yet, Marseille struck twice in the closing moments to take a surprise lead. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a breathtaking turn of events, the Portuguese striker snatched a vital leveler in the dying moments to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping crucial kicks from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing shootout win.
Now 14-time champions PSG, who faced last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now won this trophy for the twelfth time in the past 13 seasons.