The Parisian club has now secured the prestigious cup on fourteen separate times.
Paris Saint-Germain needed 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 victory.
The European champions appeared to be sailing towards a straightforward win in the showdown between the French league winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, Marseille struck twice in the closing moments to take a shock advantage. Initially, the English forward 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 snatched a crucial leveler in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and the young talent all converted with composure for Paris Saint-Germain to seal a 4-1 penalty win.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the last thirteen years.