PSG has now secured the prestigious trophy on 14 separate occasions.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in Kuwait and capture a fourth straight 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 Coupe de France winners after Ousmane Dembele opened the net early on.
However, Marseille fired twice late to take a surprise lead. First, Mason Greenwood converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own-goal.
In a remarkable twist of fortune, Goncalo Ramos grabbed a crucial leveler in the final moments to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, stopping crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, the full-back, and the young talent all converted successfully for Paris Saint-Germain to complete a convincing shootout win.
Now 14-time winners Paris Saint-Germain, who met 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 past 13 seasons.