PSG has now won the prestigious cup on 14 separate occasions.
The Parisian giants needed a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a straightforward win in the match between the French league winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, Marseille fired twice late to take a surprise 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 twist of events, Goncalo Ramos grabbed a crucial leveler in the final moments to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving crucial attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and the young talent all scored successfully for PSG to seal a convincing shootout win.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the past 13 years.