The Parisian club has now claimed the season-opening cup on 14 separate occasions.
Paris Saint-Germain needed a dramatic 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 European champions seemed to be sailing towards a comfortable win in the showdown featuring the French league winners and the Coupe de France holders after the French winger found the scoring in the opening stages.
Yet, Marseille struck twice late to take 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 snatched a crucial equaliser in the final seconds to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted with composure for Paris Saint-Germain to seal a 4-1 shootout win.
The record champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now won this competition for the twelfth time in the last 13 seasons.
