The Parisian club has now claimed the season-opening cup on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a successful spot-kick decider to get past Marseille in the Gulf and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders seemed to be coasting towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the French Cup winners after Ousmane Dembele opened the scoring early on.
However, the southern French side struck twice in the closing moments to take a shock advantage. Initially, the English forward converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a vital equaliser in the final moments to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving crucial attempts from O'Riley and Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to complete a 4-1 penalty victory.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the last 13 years.