The Parisian club has now secured the prestigious cup on 14 separate times.
The Parisian giants required a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a straightforward triumph in the match featuring the French league champions and the French Cup holders after Ousmane Dembele found the scoring early on.
However, Marseille struck twice in the closing moments to seize a surprise lead. First, the English forward converted from the penalty spot, before the defender inadvertently directed the ball into his own net for an own-goal.
In a remarkable turn of events, the Portuguese striker snatched a crucial leveler in the final seconds to force the match into a penalty shootout. The Parisian shot-stopper Chevalier then emerged as the hero, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for PSG to seal a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the last 13 seasons.