The Parisian club has now claimed the season-opening trophy on 14 separate times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful spot-kick decider to get past Marseille in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders appeared to be sailing towards a straightforward win in the match between the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired two times late to seize a surprise advantage. Initially, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a crucial leveler in the final moments to force the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the hero, stopping decisive attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all scored with composure for PSG to seal a convincing penalty victory.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now lifted this competition for the 12th time in the last 13 years.
