The Parisian club has now claimed the prestigious trophy on 14 separate times.
The Parisian giants required a dramatic equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and secure a fourth straight French Super Cup victory.
The European champions seemed to be coasting towards a straightforward triumph in the match featuring the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the net in the opening stages.
However, Marseille struck twice late to take a shock lead. First, Mason Greenwood scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own-goal.
In a breathtaking twist of fortune, the Portuguese striker grabbed a crucial leveler in the final seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving crucial attempts from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored successfully for PSG to seal a convincing shootout victory.
Now 14-time champions 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 won this competition for the twelfth time in the last 13 seasons.