The Parisian club has now claimed the prestigious trophy on 14 different times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful penalty shootout to get past 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 showdown featuring the French league champions and the Coupe de France holders after Ousmane Dembele found the net early on.
Yet, Marseille fired two times in the closing moments to take a surprise advantage. First, Mason Greenwood converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of events, Goncalo Ramos snatched a vital leveler in the final moments to force the match into a penalty shootout. PSG goalkeeper Chevalier then emerged as the key figure, stopping decisive kicks from O'Riley and Traore.
In the shootout, Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for PSG to complete a 4-1 penalty victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the past 13 years.
