The Parisian club has now claimed the prestigious trophy on 14 different occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the Coupe de France holders after the French winger opened the scoring in the opening stages.
Yet, Marseille struck twice late to take a shock lead. Initially, the English forward scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a vital equaliser in the dying moments to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving decisive kicks from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for PSG to seal a convincing shootout win.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past 13 years.