The Parisian club has now claimed the prestigious trophy on fourteen separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the match between the Ligue 1 winners and the Coupe de France holders after the French winger found the net early on.
However, Marseille struck two times late to seize a shock lead. First, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a breathtaking twist of events, the Portuguese striker grabbed a crucial leveler in the dying moments to force the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving crucial attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored with composure for PSG to seal a convincing penalty win.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the past 13 seasons.