The Parisian club has now claimed the prestigious trophy on fourteen separate times.
Paris Saint-Germain required a stoppage-time leveler followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and capture a fourth straight French Super Cup victory.
The European champions seemed to be sailing towards a straightforward triumph in the match between the French league winners and the French Cup winners after Ousmane Dembele opened the net early on.
However, Marseille struck two times in the closing moments to seize a surprise lead. First, the English forward converted from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, the Portuguese striker snatched a vital leveler in the dying moments to force the match into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the key figure, stopping crucial kicks from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for Paris Saint-Germain to complete a convincing shootout win.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now won this trophy for the twelfth time in the last thirteen seasons.