PSG has now won the prestigious cup on 14 different occasions.
The Parisian giants required a stoppage-time leveler followed by a perfect penalty shootout to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive Trophee des Champions victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown between the French league champions and the Coupe de France winners after Ousmane Dembele found the net early on.
However, Marseille struck two times late to seize a surprise lead. First, the English forward scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of fortune, Goncalo Ramos grabbed a vital leveler in the dying moments to force the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving crucial attempts from O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for PSG to seal a convincing penalty win.
Now 14-time winners PSG, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the past 13 years.