The Parisian club has now won the prestigious trophy on 14 different times.
Paris Saint-Germain needed a dramatic leveler followed by a perfect spot-kick decider to get past Marseille in Kuwait and capture a fourth straight Trophee des Champions victory.
The European champions seemed to be sailing towards a straightforward win in the match featuring the Ligue 1 champions and the French Cup holders after the French winger opened the net early on.
However, Marseille fired two times late to seize a shock advantage. First, the English forward scored from the penalty spot, before the defender unfortunately directed the ball into his own net for an own-goal.
In a breathtaking twist of fortune, Goncalo Ramos grabbed a crucial equaliser in the dying seconds to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, stopping decisive attempts from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to complete a 4-1 penalty victory.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now lifted this competition for the twelfth time in the past 13 years.