PSG has now claimed the season-opening cup on 14 separate times.
The Parisian giants required a stoppage-time leveler 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 appeared to be sailing towards a straightforward win in the showdown between the French league winners and the French Cup holders after Ousmane Dembele opened the net early on.
However, Marseille fired two times in the closing moments to seize a surprise advantage. First, the English forward converted from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a vital leveler in the dying seconds to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive kicks from O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and the young talent all converted successfully for PSG to seal a convincing shootout victory.
Now 14-time champions PSG, who met last season's Ligue 1 runners-up Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the past thirteen years.