The Parisian club has now won the season-opening trophy on fourteen different occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable triumph in the showdown between the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the scoring early on.
However, Marseille fired twice in the closing moments to take a surprise advantage. Initially, Mason Greenwood scored from the spot-kick, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a breathtaking twist of fortune, the Portuguese striker snatched a vital equaliser in the final seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving crucial kicks from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all converted successfully for PSG to complete a 4-1 penalty win.
The record champions PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now lifted this trophy for the 12th time in the last 13 seasons.