PSG has now won the prestigious trophy on fourteen separate occasions.
The Parisian giants needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup victory.
The European champions appeared to be coasting towards a comfortable triumph in the match between the French league champions and the Coupe de France holders after the French winger opened the net in the opening stages.
However, Marseille struck two times in the closing moments to take a shock advantage. Initially, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of fortune, the Portuguese striker grabbed a crucial leveler in the dying moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted successfully for Paris Saint-Germain to seal a 4-1 shootout win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now won this competition for the 12th time in the past 13 seasons.