The Parisian club has now won the prestigious cup on fourteen separate times.
Paris Saint-Germain needed a dramatic leveler 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 European champions appeared to be sailing towards a straightforward triumph in the match between the French league winners and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille fired two times in the closing moments to seize a shock lead. First, the English forward scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, the Portuguese striker snatched a vital leveler in the dying seconds to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to seal a 4-1 shootout win.
Now 14-time winners PSG, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the past thirteen seasons.