The Parisian club has now won the prestigious trophy on 14 separate times.
Paris Saint-Germain required a stoppage-time equaliser 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 appeared to be sailing towards a comfortable triumph in the match between the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired twice late to seize a shock advantage. Initially, Mason Greenwood scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a breathtaking twist of fortune, the Portuguese striker snatched a crucial equaliser in the final moments to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping decisive attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for Paris Saint-Germain to complete a 4-1 penalty win.
Now 14-time winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this competition for the 12th time in the last 13 years.
