PSG has now won the season-opening cup on 14 different times.
The Parisian giants needed a stoppage-time leveler followed by a successful spot-kick decider to overcome Marseille in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The European champions appeared to be sailing towards a comfortable win in the showdown featuring the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille struck two times late to seize a surprise lead. First, Mason Greenwood converted 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 grabbed a vital equaliser in the dying moments to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving decisive attempts from O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to seal a 4-1 penalty win.
The record champions PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now won this trophy for the twelfth time in the last thirteen seasons.