PSG has now claimed the prestigious cup on 14 separate times.
The Parisian giants required a dramatic equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders appeared to be sailing towards a comfortable triumph in the match between the French league champions and the Coupe de France winners after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille fired two times in the closing moments to take a shock advantage. Initially, the English forward scored from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, Goncalo Ramos grabbed a vital equaliser in the dying seconds to send the contest into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the hero, stopping crucial kicks from O'Riley and Traore.
In the shootout, Ramos, Vitinha, the full-back, and the young talent all converted successfully for PSG to seal a 4-1 shootout victory.
Now 14-time champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this competition for the twelfth time in the past thirteen seasons.