PSG has now claimed the prestigious cup on 14 different occasions.
Paris Saint-Germain required a stoppage-time leveler followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight Trophee des Champions title.
The European champions appeared to be coasting towards a comfortable win in the match between the French league winners and the Coupe de France holders after the French winger found the net early on.
However, Marseille struck twice in the closing moments to take a surprise lead. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately directed the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos grabbed a vital equaliser in the dying moments to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all converted with composure for Paris Saint-Germain to complete a convincing shootout win.
The record winners PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a domestic double, have now lifted this trophy for the 12th time in the past thirteen years.