PSG has now secured the prestigious cup on 14 different occasions.
The Parisian giants required a dramatic leveler followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be coasting towards a straightforward win in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the net early on.
Yet, Marseille struck twice in the closing moments to seize a shock advantage. Initially, Mason Greenwood converted from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a crucial equaliser in the dying moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping crucial kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and the young talent all converted with composure for Paris Saint-Germain to complete a 4-1 shootout win.
Now 14-time winners PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this competition for the twelfth time in the past thirteen years.