The Parisian club has now won the prestigious cup on 14 separate occasions.
Paris Saint-Germain needed a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a record-extending fourth consecutive Trophee des Champions victory.
The European champions seemed to be sailing towards a straightforward win in the match featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele opened the net early on.
However, Marseille fired twice in the closing moments to seize a shock advantage. Initially, the English forward scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a breathtaking turn of fortune, the Portuguese striker grabbed a vital equaliser in the final seconds to force the match into a deciding shootout. PSG goalkeeper Chevalier then stood as the key figure, stopping decisive attempts from O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for Paris Saint-Germain to complete a 4-1 penalty victory.
Now 14-time champions PSG, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the last thirteen years.