PSG has now claimed the season-opening cup 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 fourth straight French Super Cup victory.
The European champions appeared to be coasting towards a straightforward win in the match between the French league champions and the Coupe de France holders after Ousmane Dembele found the net early on.
Yet, Marseille struck two times in the closing moments to seize a shock advantage. First, the English forward converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a vital leveler in the final seconds to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored with composure for Paris Saint-Germain to seal a convincing penalty victory.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the last 13 seasons.