The Parisian club has now claimed the prestigious cup on 14 separate times.
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 Trophee des Champions victory.
The European champions seemed to be sailing towards a comfortable triumph in the match between the French league winners and the Coupe de France holders after the French winger opened the scoring in the opening stages.
Yet, Marseille fired twice in the closing moments to seize a shock advantage. First, Mason Greenwood converted from the spot-kick, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos grabbed a crucial leveler in the dying seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, the full-back, and the young talent all converted with composure for Paris Saint-Germain to seal a 4-1 shootout win.
The record winners PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now lifted this trophy for the twelfth time in the past thirteen seasons.