The Parisian club has now won the prestigious cup on fourteen separate times.
Paris Saint-Germain required a stoppage-time 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 victory.
The Champions League holders appeared to be sailing towards a straightforward win in the match featuring the French league winners and the Coupe de France holders after Ousmane Dembele opened the net early on.
Yet, Marseille fired two times in the closing moments to take a shock lead. First, the English forward scored from the spot-kick, 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 leveler in the dying seconds to send the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for PSG to seal a convincing shootout victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the last thirteen seasons.