PSG has now won the prestigious cup on 14 different times.
The Parisian giants required a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive Trophee des Champions title.
The Champions League holders seemed to be sailing towards a comfortable 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.
Yet, Marseille struck two times in the closing moments to take a shock advantage. Initially, Mason Greenwood scored from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, Goncalo Ramos grabbed a vital leveler in the final seconds to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all converted with composure for PSG to seal a convincing shootout win.
The record winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the last thirteen seasons.