PSG has now claimed the season-opening trophy on 14 separate occasions.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward win in the match featuring the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
However, Marseille fired twice in the closing moments to seize a surprise lead. First, Mason Greenwood scored from the spot-kick, before the defender inadvertently 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 moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and the young talent all scored successfully for Paris Saint-Germain to complete a convincing penalty win.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this trophy for the twelfth time in the past 13 seasons.