The Parisian club has now claimed the prestigious trophy on 14 different occasions.
The Parisian giants needed a stoppage-time leveler followed by a perfect penalty shootout to get past Marseille in Kuwait and capture a fourth straight Trophee des Champions title.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 champions and the Coupe de France winners after Ousmane Dembele opened the scoring in the opening stages.
However, the southern French side struck two times late to seize a shock lead. First, the English forward converted from the penalty spot, before Willian Pacho inadvertently directed the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos grabbed a crucial leveler in the final seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored successfully 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 Olympique de Marseille after completing a league and cup double, have now won this competition for the 12th time in the last thirteen seasons.