The Parisian club has now secured the prestigious trophy on 14 different occasions.
The Parisian giants needed a dramatic equaliser followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown featuring the French league champions and the Coupe de France holders after the French winger found the scoring early on.
However, Marseille fired twice in the closing moments to take a surprise advantage. First, the English forward converted from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable turn of events, Goncalo Ramos snatched a vital leveler in the dying moments to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for Paris Saint-Germain to seal a convincing penalty win.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the past 13 years.