The Parisian club has now claimed the prestigious trophy on fourteen separate times.
Paris Saint-Germain needed a dramatic equaliser followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders seemed to be sailing towards a comfortable win in the match between the French league champions and the French Cup holders after the French winger found the net early on.
Yet, Marseille struck twice in the closing moments to take a shock lead. First, Mason Greenwood converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a vital leveler in the dying moments to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for PSG to seal a 4-1 penalty win.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the past 13 seasons.
