The Parisian club has now won the season-opening cup on 14 different occasions.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and secure a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable win in the match between the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele opened the net early on.
Yet, Marseille fired two times late to seize a shock lead. First, Mason Greenwood converted from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of events, Goncalo Ramos snatched a crucial leveler in the dying moments to send the contest into a penalty 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, Vitinha, the full-back, and the young talent all scored with composure 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 lifted this trophy for the 12th time in the last thirteen seasons.