The Parisian club has now claimed the season-opening cup on fourteen separate occasions.
The Parisian giants needed a stoppage-time leveler followed by a perfect spot-kick decider to get past their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele found the scoring early on.
However, Marseille struck twice in the closing moments to seize a shock advantage. Initially, Mason Greenwood scored from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a crucial equaliser in the dying seconds to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted with composure for PSG to seal a 4-1 shootout victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this trophy for the twelfth time in the last thirteen years.