The Parisian club has now claimed the prestigious cup on 14 different times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a straightforward win in the match between the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele found the net early on.
However, Marseille struck two times late to take a surprise lead. Initially, the English forward converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a crucial equaliser in the dying moments to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for Paris Saint-Germain to seal a 4-1 shootout win.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past 13 years.