The Parisian club has now secured the prestigious cup on fourteen different times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight Trophee des Champions victory.
The European champions appeared to be sailing towards a comfortable win in the showdown between the French league champions and the Coupe de France holders after the French winger opened the scoring early on.
Yet, Marseille fired twice late to seize a surprise lead. First, Mason Greenwood converted from the spot-kick, before the defender unfortunately directed the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a vital leveler in the final seconds to force the contest into a deciding shootout. PSG goalkeeper Chevalier then stood as the hero, stopping decisive kicks from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for PSG to seal a convincing shootout victory.
The record champions PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the twelfth time in the last thirteen years.
