The Parisian club has now claimed the prestigious trophy on 14 separate occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable win in the showdown between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired twice late to seize a surprise lead. First, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a vital equaliser in the dying moments to force the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for Paris Saint-Germain to complete a 4-1 shootout victory.
The record champions PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the past thirteen years.