The Parisian club has now secured the prestigious trophy on 14 separate occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a successful penalty shootout to get past their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable triumph in the showdown between the Ligue 1 champions and the French Cup holders after the French winger opened the net in the opening stages.
However, Marseille fired two times late to seize a shock advantage. First, Mason Greenwood converted from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable twist of events, the Portuguese striker grabbed a crucial leveler in the dying moments to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted successfully for PSG to seal a 4-1 shootout victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now lifted this competition for the twelfth time in the last thirteen years.