The Parisian club has now claimed the season-opening cup on fourteen separate occasions.
The Parisian giants required a dramatic leveler 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 European champions seemed to be sailing towards a straightforward win in the showdown between the Ligue 1 winners and the Coupe de France winners after Ousmane Dembele found the scoring early on.
However, Marseille struck twice in the closing moments to take a shock lead. Initially, the English forward scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own-goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a vital equaliser in the dying moments to send the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and the young talent all scored with composure for Paris Saint-Germain to seal a convincing penalty victory.
The record winners PSG, who met last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now lifted this competition for the 12th time in the past 13 seasons.