PSG has now claimed the prestigious trophy on 14 separate times.
Paris Saint-Germain needed a dramatic leveler followed by a successful penalty shootout to get past their arch-rivals in Kuwait and secure a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a comfortable triumph in the match between the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
Yet, Marseille fired twice in the closing moments to seize a shock lead. Initially, Mason Greenwood scored from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker grabbed a vital equaliser in the final moments to force the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping crucial attempts from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for Paris Saint-Germain to complete a 4-1 shootout win.
The record winners PSG, who met last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this trophy for the twelfth time in the last 13 seasons.