The Parisian club has now won the prestigious cup on 14 separate times.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive Trophee des Champions title.
The European champions appeared to be coasting towards a straightforward triumph in the match between the French league winners and the French Cup holders after Ousmane Dembele found the scoring in the opening stages.
However, Marseille struck twice in the closing moments to take a shock lead. Initially, the English forward converted from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a remarkable twist of events, Goncalo Ramos snatched a vital leveler in the dying moments to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving decisive kicks from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted with composure for Paris Saint-Germain to seal a convincing penalty win.
The record champions PSG, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the last 13 seasons.
