The Parisian club has now secured the prestigious trophy on fourteen different times.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the match between the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring early on.
However, Marseille fired twice in the closing moments to seize a surprise lead. Initially, Mason Greenwood scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of fortune, the Portuguese striker snatched a crucial equaliser in the final moments to force the match into a deciding shootout. PSG goalkeeper Chevalier then emerged as the key figure, stopping crucial attempts from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored with composure for PSG to complete a 4-1 penalty win.
The record winners PSG, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this trophy for the twelfth time in the past thirteen seasons.