The Parisian club has now secured the prestigious trophy on 14 separate times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful penalty shootout to get past Marseille in Kuwait and capture a fourth straight French Super Cup victory.
The European champions seemed to be coasting towards a straightforward win in the showdown between the Ligue 1 champions and the Coupe de France holders after Ousmane Dembele opened the scoring in the opening stages.
However, Marseille fired twice in the closing moments to seize a surprise advantage. First, the English forward converted from the spot-kick, before Willian Pacho inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a crucial leveler in the final moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Ramos, the midfielder, Nuno Mendes, and Desire Doue all converted successfully for Paris Saint-Germain to seal 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 trophy for the twelfth time in the past thirteen seasons.