PSG has now secured the prestigious trophy on 14 different times.
The Parisian giants required a stoppage-time leveler followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a straightforward win in the showdown featuring the Ligue 1 champions and the French Cup winners after the French winger opened the net early on.
However, Marseille fired two times late to seize a surprise 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 turn of fortune, Goncalo Ramos snatched a crucial equaliser in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive attempts from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal a convincing penalty win.
The record winners PSG, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this competition for the twelfth time in the last thirteen seasons.
