PSG has now claimed the prestigious trophy on 14 different times.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a straightforward win in the showdown between the Ligue 1 champions and the French Cup holders after Ousmane Dembele found the net in the opening stages.
However, Marseille struck two times in the closing moments to seize a surprise lead. Initially, the English forward converted from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable twist of events, the Portuguese striker snatched a crucial equaliser in the final moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, 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 win.
Now 14-time champions PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now won this competition for the 12th time in the last 13 seasons.