The Parisian club has now secured the prestigious cup on fourteen different times.
Paris Saint-Germain required a dramatic equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward win in the match between the French league winners and the Coupe de France holders after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille struck twice late to take a shock advantage. Initially, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a crucial leveler in the final moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted with composure for PSG to complete a convincing penalty win.
The record champions PSG, who faced last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now lifted this competition for the twelfth time in the last thirteen seasons.