PSG has now claimed the prestigious trophy on fourteen different occasions.
The Parisian giants needed a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be coasting towards a comfortable win in the match between the French league champions and the French Cup holders after Ousmane Dembele found the scoring in the opening stages.
However, Marseille struck twice late to seize a surprise lead. First, Mason Greenwood converted from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a breathtaking twist of events, Goncalo Ramos snatched a crucial equaliser in the final seconds to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, stopping decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to seal a 4-1 penalty victory.
The record winners PSG, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the past thirteen years.
