PSG has now won the prestigious cup on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight Trophee des Champions title.
The Champions League holders seemed to be sailing towards a comfortable win in the showdown between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille fired two times in the closing moments to take a shock advantage. Initially, the English forward converted from the penalty spot, before Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a vital equaliser in the dying seconds to send the match into a deciding shootout. The Parisian shot-stopper Chevalier then stood as the key figure, stopping decisive kicks from O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for PSG to complete a 4-1 shootout win.
The record champions PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past thirteen seasons.