The Parisian club has now secured the prestigious cup on 14 different times.
The Parisian giants needed a dramatic leveler followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be coasting towards a straightforward win in the showdown featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring early on.
However, Marseille fired twice late to take a shock lead. Initially, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a vital equaliser in the final seconds to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial attempts from O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all scored with composure for Paris Saint-Germain to seal a convincing shootout victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this trophy for the twelfth time in the past thirteen seasons.
