The Parisian club has now claimed 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 their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be sailing towards a comfortable triumph in the showdown featuring the French league winners and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille struck twice in the closing moments to take a shock advantage. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos grabbed a vital equaliser in the final seconds to force the match into a penalty shootout. The Parisian shot-stopper Chevalier then stood as the hero, saving crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for Paris Saint-Germain to complete a 4-1 shootout win.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the past thirteen seasons.