The Parisian club has now secured the prestigious cup on 14 separate occasions.
The Parisian giants required a stoppage-time equaliser followed by a perfect spot-kick decider 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 featuring the French league winners and the Coupe de France winners after the French winger opened the net in the opening stages.
Yet, Marseille struck twice in the closing moments to seize a surprise advantage. First, Mason Greenwood converted from the penalty spot, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker grabbed a vital equaliser in the final seconds to force the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and the young talent all scored with composure for Paris Saint-Germain to complete a convincing penalty win.
The record winners Paris Saint-Germain, who met last season's Ligue 1 second-placed team Olympique de Marseille after achieving a league and cup double, have now lifted this competition for the 12th time in the past thirteen years.