The Parisian club has now won the prestigious trophy on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a successful spot-kick decider to overcome 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 triumph in the showdown featuring the French league champions and the Coupe de France winners after Ousmane Dembele found the net early on.
However, Marseille struck two times in the closing moments to take a shock lead. First, the English forward scored from the spot-kick, before the defender unfortunately directed the ball into his own net for an own-goal.
In a breathtaking turn of fortune, the Portuguese striker snatched a vital leveler in the final moments to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving crucial attempts from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for PSG to complete a 4-1 shootout victory.
The record winners PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this competition for the 12th time in the past 13 seasons.