PSG has now won the prestigious trophy on fourteen separate times.
Paris Saint-Germain required a stoppage-time leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a fourth straight French Super Cup title.
The Champions League holders appeared to be coasting towards a comfortable win in the match between the French league winners and the French Cup holders after Ousmane Dembele found the scoring early on.
However, Marseille fired twice late to take a surprise advantage. Initially, Mason Greenwood scored from the penalty spot, before the defender inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of events, Goncalo Ramos grabbed a crucial equaliser in the dying seconds to force the contest into a penalty shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, stopping decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all converted with composure for Paris Saint-Germain to seal a 4-1 shootout win.
The record champions PSG, who faced last season's Ligue 1 runners-up Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past thirteen years.