PSG has now claimed the season-opening trophy on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be coasting towards a straightforward triumph in the showdown featuring the French league winners and the Coupe de France winners after Ousmane Dembele found the net in the opening stages.
However, Marseille fired two times late to seize a surprise lead. First, Mason Greenwood converted from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a vital equaliser in the dying moments to force the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the hero, saving crucial kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for Paris Saint-Germain to seal a convincing shootout win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this competition for the twelfth time in the last 13 seasons.