The Parisian club has now won the prestigious trophy on 14 different occasions.
The Parisian giants needed a stoppage-time leveler followed by a perfect penalty shootout to overcome Marseille in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the scoring in the opening stages.
Yet, the southern French side fired twice late to seize a shock lead. First, 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 turn of events, Goncalo Ramos grabbed a vital leveler in the final moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to seal a convincing penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the last 13 years.