The Parisian club has now claimed the prestigious cup on 14 different times.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and secure a record-extending fourth consecutive Trophee des Champions title.
The Champions League holders appeared to be coasting towards a straightforward win in the match between the Ligue 1 champions and the French Cup winners after the French winger opened the scoring early on.
Yet, Marseille fired twice in the closing moments to take a shock advantage. Initially, the English forward scored from the spot-kick, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a breathtaking turn of events, the Portuguese striker grabbed a crucial equaliser in the final seconds to force the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the hero, saving decisive attempts from Matt O'Riley and Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted with composure for PSG to seal a convincing penalty victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now won this competition for the twelfth time in the last 13 years.
