The Parisian club has now claimed the prestigious trophy on 14 different times.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to overcome Marseille in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be sailing towards a straightforward win in the showdown between the Ligue 1 winners and the French Cup holders after the French winger found the net early on.
However, Marseille struck two times in the closing moments to seize a shock lead. Initially, the English forward converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable twist of events, Goncalo Ramos grabbed a crucial equaliser in the dying moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all converted with composure for PSG to complete a convincing penalty win.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a domestic double, have now won this trophy for the twelfth time in the last thirteen seasons.