The Parisian club has now won the season-opening cup on 14 different times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful penalty shootout to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the net early on.
However, Marseille struck two times late to seize a shock lead. Initially, the English forward scored from the penalty spot, before the defender inadvertently directed the ball into his own net for an own-goal.
In a breathtaking twist of fortune, the Portuguese striker grabbed a crucial equaliser in the dying moments to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for PSG to seal a convincing penalty win.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the last thirteen seasons.