The Parisian club has now claimed the prestigious cup on 14 different occasions.
The Parisian giants needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The European champions appeared to be sailing towards a straightforward win in the match featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring early on.
However, Marseille fired two times in the closing moments to take a surprise lead. First, Mason Greenwood converted from the penalty spot, before the defender inadvertently directed the ball into his own net for an own goal.
In a breathtaking twist of events, the Portuguese striker grabbed a crucial equaliser in the dying seconds to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted successfully for Paris Saint-Germain to seal a 4-1 penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a domestic double, have now lifted this trophy for the twelfth time in the last 13 years.