PSG has now secured the season-opening 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 secure a fourth straight French Super Cup victory.
The Champions League holders seemed to be coasting towards a straightforward triumph in the match between the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille struck two times in the closing moments to seize a surprise advantage. Initially, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a remarkable twist of events, the Portuguese striker snatched a vital leveler in the dying seconds to force the contest into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all scored successfully for Paris Saint-Germain to seal a convincing penalty victory.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now won this trophy for the 12th time in the last 13 seasons.