The Parisian club has now claimed the prestigious trophy on 14 different occasions.
Paris Saint-Germain needed a dramatic leveler followed by a perfect 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 straightforward triumph in the match featuring the Ligue 1 champions and the French Cup holders after Ousmane Dembele found the scoring early on.
However, Marseille struck twice in the closing moments to take a shock advantage. First, the English forward converted from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own-goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a vital leveler in the dying moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, stopping crucial kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted with composure for Paris Saint-Germain to complete a convincing shootout win.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the last 13 years.