The Parisian club has now secured the season-opening cup on 14 separate occasions.
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 sailing towards a comfortable win in the showdown between the Ligue 1 champions and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, Marseille fired two times in the closing moments to take a shock advantage. First, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a breathtaking twist of fortune, the Portuguese striker snatched a crucial leveler in the dying seconds to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving crucial kicks from O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all converted successfully for PSG to seal a convincing penalty victory.
The record champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a domestic double, have now won this competition for the twelfth time in the past thirteen seasons.