The Parisian club has now won the prestigious cup on 14 different occasions.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive Trophee des Champions title.
The European champions appeared to be sailing towards a straightforward win in the match featuring the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring early on.
Yet, Marseille fired two times in the closing moments to seize a shock lead. Initially, Mason Greenwood scored from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own goal.
In a remarkable twist of fortune, the Portuguese striker grabbed a crucial leveler in the final seconds to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping crucial attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to seal a 4-1 penalty win.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this trophy for the twelfth time in the past thirteen seasons.