The Parisian club has now claimed the prestigious trophy on 14 different times.
The Parisian giants required a stoppage-time leveler followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the French Cup holders after Ousmane Dembele found the net early on.
However, Marseille fired twice late to seize a surprise advantage. Initially, the English forward converted from the spot-kick, before the defender unfortunately 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 moments to send the match into a penalty shootout. The Parisian shot-stopper Chevalier then emerged as the hero, stopping decisive attempts from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all converted with composure for Paris Saint-Germain to complete a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past thirteen years.