The Parisian club has now won the prestigious trophy on fourteen separate occasions.
Paris Saint-Germain required a dramatic equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be sailing towards a straightforward win in the showdown featuring the French league champions and the Coupe de France holders after Ousmane Dembele found the net in the opening stages.
However, Marseille fired twice in the closing moments to seize a shock 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 twist of events, Goncalo Ramos grabbed a crucial equaliser in the dying seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for PSG to complete a convincing shootout victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now won this trophy for the twelfth time in the last thirteen seasons.