The Parisian club has now claimed the season-opening trophy on 14 separate occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders seemed to be coasting towards a comfortable win in the showdown between the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring early on.
However, Marseille fired twice in the closing moments to seize a shock lead. First, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a crucial equaliser in the final seconds to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial attempts from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted with composure for PSG to complete a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this competition for the twelfth time in the last thirteen seasons.