The Parisian club has now claimed the prestigious cup on fourteen different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders appeared to be coasting towards a comfortable triumph in the match between the Ligue 1 champions and the Coupe de France winners after the French winger found the scoring in the opening stages.
Yet, Marseille fired twice in the closing moments to take a shock lead. First, Mason Greenwood converted from the spot-kick, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, the Portuguese striker grabbed a vital equaliser in the final moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving crucial attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for Paris Saint-Germain to seal a convincing 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 twelfth time in the past 13 years.