The Parisian club has now secured the prestigious trophy on fourteen separate times.
Paris Saint-Germain required 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 coasting towards a comfortable triumph in the showdown featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net early on.
However, the southern French side fired two times late to seize a surprise lead. Initially, the English forward converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable twist of events, the Portuguese striker snatched a crucial leveler in the final seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving decisive attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent 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 achieving a league and cup double, have now lifted this trophy for the twelfth time in the last 13 years.