The Parisian club has now won the prestigious cup on fourteen different times.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a straightforward triumph in the match between the French league winners and the French Cup winners after Ousmane Dembele opened the net early on.
Yet, Marseille fired two times in the closing moments to seize a surprise advantage. Initially, the English forward converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a crucial equaliser in the dying seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to complete a 4-1 shootout win.
Now 14-time champions PSG, 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 years.