The Parisian club has now claimed the season-opening cup on fourteen different times.
The Parisian giants required a dramatic leveler followed by a successful penalty shootout to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be sailing towards a straightforward win in the match featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille fired two times in the closing moments to take a surprise advantage. 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 breathtaking twist of fortune, the Portuguese striker grabbed a vital equaliser in the final moments to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to seal a convincing penalty victory.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now won this competition for the 12th time in the past 13 years.