PSG has now secured the season-opening trophy on 14 separate occasions.
The Parisian giants required a stoppage-time equaliser followed by a successful penalty shootout to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be sailing towards a straightforward win in the showdown between the Ligue 1 champions and the French Cup holders after the French winger found the net in the opening stages.
Yet, Marseille fired two times late to take a surprise lead. First, the English forward scored from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking turn of events, the Portuguese striker snatched a crucial equaliser in the final moments to send the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the key figure, stopping decisive kicks from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored with composure for Paris Saint-Germain 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 domestic double, have now lifted this trophy for the twelfth time in the last 13 seasons.