PSG has now claimed the prestigious cup on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a comfortable triumph in the match featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele found the scoring early on.
However, Marseille struck twice late to seize a surprise advantage. First, the English forward 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 events, Goncalo Ramos grabbed a vital leveler in the final seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, the full-back, and the young talent all scored successfully for PSG to seal a convincing shootout win.
Now 14-time champions 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 twelfth time in the past 13 seasons.
