The Parisian club has now won the prestigious cup on 14 different times.
Paris Saint-Germain 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 European champions seemed to be sailing towards a comfortable triumph in the match between the Ligue 1 champions and the French Cup holders after Ousmane Dembele found the scoring early on.
Yet, Marseille struck two times late to take a surprise advantage. Initially, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos grabbed a crucial equaliser in the dying seconds to force the contest into a penalty shootout. PSG goalkeeper Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and the young talent all scored successfully for PSG to complete a convincing penalty win.
Now 14-time winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now won this trophy for the 12th time in the last thirteen years.