The Parisian club has now claimed the season-opening cup on fourteen different times.
The Parisian giants needed a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight Trophee des Champions victory.
The Champions League holders appeared to be coasting towards a straightforward triumph in the showdown featuring the French league winners and the Coupe de France winners after the French winger opened the net early on.
Yet, Marseille struck twice in the closing moments to take a shock lead. First, the English forward converted from the spot-kick, before the defender inadvertently turned the ball into his own net for an own-goal.
In a breathtaking twist of events, Goncalo Ramos snatched a crucial leveler in the final moments to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored with composure for PSG to seal a convincing penalty victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this trophy for the twelfth time in the past 13 seasons.