The Parisian club has now secured the season-opening cup on 14 different times.
The Parisian giants needed a dramatic equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and secure a fourth straight Trophee des Champions victory.
The Champions League holders seemed to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the scoring in the opening stages.
Yet, Marseille struck two times in the closing moments to take a shock advantage. First, the English forward converted from the spot-kick, before the defender inadvertently directed the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos snatched a vital equaliser in the dying seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, saving decisive attempts from Matt O'Riley and Traore.
From the spot, Ramos, the midfielder, the full-back, and the young talent all converted with composure for Paris Saint-Germain to complete a 4-1 penalty victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this trophy for the twelfth time in the last thirteen seasons.