The Parisian club has now secured the prestigious cup on fourteen separate occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a comfortable win in the showdown between the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the scoring early on.
Yet, Marseille fired two times late to seize a surprise advantage. Initially, the English forward converted from the penalty spot, before the defender inadvertently turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, the Portuguese striker snatched a crucial leveler in the dying moments to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, stopping decisive attempts from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for Paris Saint-Germain to complete a 4-1 shootout victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now lifted this competition for the twelfth time in the last 13 years.