PSG has now claimed the prestigious cup on 14 separate occasions.
The Parisian giants needed a stoppage-time leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable triumph in the match featuring the Ligue 1 winners and the Coupe de France winners after the French winger opened the scoring early on.
Yet, Marseille fired twice late to take a surprise advantage. Initially, Mason Greenwood scored from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, the Portuguese striker snatched a vital leveler in the final seconds to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving crucial kicks from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for PSG to seal a convincing shootout victory.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this competition for the twelfth time in the past 13 seasons.