The Parisian club has now secured the prestigious trophy on 14 separate occasions.
The Parisian giants needed a stoppage-time leveler followed by a perfect spot-kick decider to get past Marseille in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a straightforward win in the showdown between the French league winners and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
Yet, Marseille fired two times late to seize a surprise lead. First, Mason Greenwood converted from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a vital leveler in the dying moments to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and the young talent all scored with composure for Paris Saint-Germain to seal a convincing shootout win.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a domestic double, have now won this competition for the twelfth time in the past thirteen seasons.