The Parisian club has now won the prestigious trophy on 14 different occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect spot-kick decider to get past Marseille in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a straightforward win in the match between the Ligue 1 winners and the French Cup holders after the French winger found the net in the opening stages.
However, Marseille struck two times late to take a shock lead. First, the English forward converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of events, Goncalo Ramos snatched a crucial leveler in the final moments to send the match into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the hero, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for PSG to complete a convincing penalty victory.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the 12th time in the last 13 seasons.