PSG has now claimed the prestigious trophy on fourteen separate times.
The Parisian giants needed a stoppage-time leveler followed by a perfect spot-kick decider to get past their arch-rivals in Kuwait and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable win in the match featuring the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele found the net early on.
However, Marseille fired two times late to take a surprise lead. First, Mason Greenwood scored from the spot-kick, before the defender unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of events, the Portuguese striker grabbed a vital leveler in the dying seconds to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving decisive kicks from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully for PSG to complete a convincing penalty victory.
Now 14-time winners PSG, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now lifted this trophy for the twelfth time in the past 13 years.