The Parisian club has now secured the season-opening cup on fourteen different times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward win in the match between the French league winners and the Coupe de France holders after Ousmane Dembele found the scoring early on.
Yet, Marseille fired twice in the closing moments to seize a shock lead. First, Mason Greenwood converted from the spot-kick, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking twist of events, Goncalo Ramos snatched a vital leveler in the final seconds to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, saving crucial kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for Paris Saint-Germain to seal a 4-1 penalty victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the past thirteen years.