PSG has now won the prestigious cup on 14 separate times.
The Parisian giants needed a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The European champions appeared to be sailing towards a comfortable win in the showdown featuring the French league champions and the Coupe de France holders after Ousmane Dembele found the net early on.
Yet, Marseille struck two times in the closing moments to seize a shock lead. Initially, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of events, Goncalo Ramos grabbed a vital leveler in the final moments to force the match into a deciding shootout. PSG goalkeeper Chevalier then stood as the key figure, stopping crucial kicks from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for PSG to seal a convincing penalty victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the past 13 years.