PSG has now secured the prestigious trophy on 14 separate occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable win in the showdown between the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the net early on.
However, Marseille struck two times in the closing moments to seize a surprise advantage. Initially, the English forward scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos grabbed a vital equaliser in the final seconds to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, stopping decisive kicks from O'Riley and Traore.
From the spot, Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for PSG to seal a 4-1 shootout win.
Now 14-time winners PSG, who faced last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the last thirteen years.