The Parisian club has now claimed the prestigious cup on 14 different times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight Trophee des Champions victory.
The Champions League holders appeared to be coasting towards a comfortable win in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille fired twice in the closing moments to seize a shock lead. Initially, the English forward scored from the penalty spot, before Willian Pacho unfortunately directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a crucial leveler in the dying moments to force the contest into a penalty shootout. The Parisian shot-stopper Chevalier then emerged as the key figure, saving crucial kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for PSG to seal a convincing shootout win.
Now 14-time winners PSG, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the last thirteen years.