The Parisian club has now won the prestigious cup on fourteen separate occasions.
The Parisian giants needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward triumph in the match featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele found the net early on.
However, Marseille struck twice in the closing moments to take a shock advantage. First, the English forward converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a crucial equaliser in the dying moments to send the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored with composure for PSG to complete a 4-1 penalty win.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now won this competition for the twelfth time in the last 13 seasons.