PSG has now claimed the prestigious trophy on fourteen different occasions.
The Parisian giants required a stoppage-time leveler followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be coasting towards a straightforward win in the match featuring the Ligue 1 champions and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille struck twice in the closing moments to take a surprise advantage. First, Mason Greenwood 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, the Portuguese striker snatched a crucial equaliser in the final seconds to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive kicks from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to complete a convincing shootout win.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this trophy for the twelfth time in the last 13 years.