The Parisian club has now claimed the prestigious trophy on 14 different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be sailing towards a comfortable win in the showdown between the French league winners and the Coupe de France winners after Ousmane Dembele found the net early on.
Yet, Marseille fired twice late to take a surprise lead. First, Mason Greenwood scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of events, Goncalo Ramos grabbed a crucial leveler in the dying moments to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping crucial attempts from O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all scored successfully for PSG to complete a 4-1 shootout win.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now lifted this trophy for the twelfth time in the past 13 years.