The Parisian club has now secured the prestigious cup on 14 different times.
The Parisian giants needed a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight Trophee des Champions title.
The European champions seemed to be coasting towards a comfortable win in the match between the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele opened the scoring early on.
Yet, Marseille struck twice in the closing moments to take a shock lead. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a crucial leveler in the final seconds to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial kicks from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully for Paris Saint-Germain to complete a 4-1 penalty win.
The record champions PSG, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the past 13 seasons.