The Parisian club has now won the prestigious cup on 14 separate times.
Paris Saint-Germain needed a dramatic equaliser followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a fourth straight Trophee des Champions title.
The Champions League holders seemed to be coasting towards a comfortable win in the match featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille struck twice late to take a surprise lead. Initially, Mason Greenwood scored from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of events, Goncalo Ramos snatched a crucial leveler in the dying moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and the young talent all converted successfully for PSG to seal a convincing shootout victory.
Now 14-time champions PSG, who faced last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now won this trophy for the 12th time in the last thirteen seasons.