The Parisian club has now claimed the season-opening cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time leveler followed by a successful spot-kick decider to overcome 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 comfortable win in the showdown between the French league winners and the French Cup winners after Ousmane Dembele opened the scoring early on.
Yet, Marseille struck two times late to seize a surprise lead. First, the English forward converted from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of events, 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 key figure, stopping decisive kicks from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and Desire Doue all converted with composure for PSG to seal a 4-1 penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a domestic double, have now won this competition for the 12th time in the past thirteen years.