The Parisian club has now claimed the prestigious trophy on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a straightforward triumph in the match featuring the Ligue 1 winners and the French Cup winners after the French winger opened the scoring in the opening stages.
However, Marseille struck twice in the closing moments to take a shock lead. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of fortune, the Portuguese striker snatched a crucial 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 O'Riley and Traore.
From the spot, Ramos, Vitinha, the full-back, and the young talent all converted successfully for PSG to complete a 4-1 shootout win.
The record winners PSG, who met last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now lifted this trophy for the twelfth time in the last thirteen years.