The Parisian club has now won the prestigious trophy on fourteen separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the French Cup holders after the French winger opened the scoring in the opening stages.
However, Marseille fired twice in the closing moments to seize a shock lead. Initially, Mason Greenwood scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a vital leveler in the dying moments to force the match into a penalty shootout. PSG goalkeeper Chevalier then stood as the hero, saving decisive attempts from O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for Paris Saint-Germain to complete a convincing shootout victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this competition for the 12th time in the past 13 seasons.