The Parisian club has now secured the prestigious cup on fourteen different occasions.
The Parisian giants needed a dramatic leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown between the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille fired two times in the closing moments to take a surprise advantage. First, the English forward converted from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of events, Goncalo Ramos grabbed a crucial equaliser in the final seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to complete a convincing penalty win.
The record winners PSG, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this trophy for the twelfth time in the past 13 seasons.