PSG has now won the season-opening trophy on 14 different times.
The Parisian giants required a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a straightforward win in the match between the Ligue 1 winners and the Coupe de France winners after the French winger opened the scoring early on.
Yet, Marseille struck twice in the closing moments to seize a shock advantage. First, the English forward converted from the spot-kick, 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 vital leveler in the final moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving crucial kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored successfully for Paris Saint-Germain to seal a convincing penalty win.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now won this competition for the 12th time in the last thirteen seasons.