PSG has now won the season-opening trophy on 14 different times.
The Parisian giants required a dramatic leveler followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward win in the showdown featuring the French league winners and the Coupe de France holders after the French winger opened the scoring in the opening stages.
Yet, Marseille fired twice in the closing moments to seize a shock advantage. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of events, Goncalo Ramos grabbed a crucial equaliser in the final seconds to force the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the key figure, saving decisive attempts from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and the young talent all converted successfully for PSG to seal a convincing penalty victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the last 13 seasons.