PSG has now won the prestigious cup on 14 separate occasions.
The Parisian giants required a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and capture a record-extending fourth consecutive Trophee des Champions title.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown between the French league winners and the Coupe de France winners after Ousmane Dembele found the net early on.
Yet, Marseille fired two times late to take a surprise advantage. Initially, the English forward scored from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a breathtaking twist of events, Goncalo Ramos grabbed a crucial equaliser in the final seconds to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to seal a convincing shootout victory.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the last thirteen seasons.