PSG has now won the prestigious trophy on fourteen separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders seemed to be coasting towards a comfortable triumph in the showdown between the French league champions and the Coupe de France winners after the French winger found the net in the opening stages.
However, Marseille fired two times late to take a surprise advantage. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of events, the Portuguese striker grabbed a crucial leveler in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed 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 shootout win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the past thirteen years.