The Parisian club has now won the prestigious trophy on 14 separate times.
Paris Saint-Germain needed a dramatic leveler followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive Trophee des Champions victory.
The European champions appeared to be coasting towards a comfortable win in the match between the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, Marseille struck two times late to take a surprise advantage. Initially, Mason Greenwood converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker snatched a crucial leveler in the final moments to send the match into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, saving decisive kicks from O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored successfully for PSG to seal a convincing penalty victory.
Now 14-time champions PSG, who met last season's Ligue 1 second-placed team Marseille after achieving a domestic double, have now won this trophy for the twelfth time in the past 13 years.