The Parisian club has now won the prestigious trophy on 14 different times.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to get past Marseille in Kuwait and capture a fourth straight French Super Cup title.
The European champions appeared to be sailing towards a comfortable triumph in the match featuring the Ligue 1 winners and the French Cup winners after the French winger opened the scoring in the opening stages.
However, Marseille struck twice late to seize a surprise lead. First, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a breathtaking twist of events, Goncalo Ramos snatched a vital leveler in the final moments to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping decisive kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing penalty victory.
Now 14-time winners PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the last thirteen years.