The Parisian club has now won the season-opening trophy on 14 different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a successful spot-kick decider 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 coasting towards a straightforward win in the showdown featuring the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring early on.
Yet, Marseille fired twice in the closing moments to seize a shock advantage. First, the English forward scored from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable turn of events, Goncalo Ramos snatched a vital leveler in the final moments to force the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving decisive kicks from O'Riley and Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and the young talent all converted successfully for PSG to complete a convincing shootout victory.
The record champions Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the last thirteen seasons.