The Parisian club has now claimed the season-opening trophy on 14 separate occasions.
The Parisian giants required a stoppage-time leveler followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders appeared to be coasting towards a straightforward triumph in the match between the French league winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, Marseille fired twice in the closing moments to seize a surprise lead. First, Mason Greenwood 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 fortune, Goncalo Ramos grabbed a crucial equaliser in the final moments to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the hero, saving decisive attempts from O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for PSG to seal a 4-1 penalty win.
The record winners PSG, who faced last season's Ligue 1 second-placed team Olympique de Marseille after achieving a domestic double, have now won this competition for the 12th time in the last 13 years.