The Parisian club has now won the prestigious cup on fourteen different times.
Paris Saint-Germain needed a stoppage-time leveler followed by a perfect 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 appeared to be sailing towards a comfortable triumph in the showdown featuring the French league champions and the French Cup winners after the French winger opened the scoring in the opening stages.
However, the southern French side struck two times in the closing moments to take a shock lead. Initially, Mason Greenwood converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a crucial leveler in the final seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, the full-back, and Desire Doue all converted with composure for PSG to complete a 4-1 penalty win.
Now 14-time winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this trophy for the twelfth time in the last thirteen seasons.