PSG has now claimed the prestigious trophy on 14 different times.
The Parisian giants needed a dramatic equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The European champions appeared to be sailing towards a straightforward triumph in the showdown between the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the net in the opening stages.
However, Marseille struck two times in the closing moments to seize a surprise advantage. First, the English forward converted from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker snatched a vital leveler in the dying seconds to force the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, stopping crucial attempts from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for PSG to seal a convincing penalty win.
Now 14-time winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the past 13 seasons.