PSG has now claimed the prestigious cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive Trophee des Champions title.
The Champions League holders seemed to be sailing towards a comfortable win in the match featuring the French league winners and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
However, Marseille fired two times late to take a surprise advantage. First, Mason Greenwood scored from the penalty spot, before the defender inadvertently 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 seconds to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for PSG to seal a convincing penalty victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now won this trophy for the twelfth time in the past 13 seasons.