PSG has now claimed the prestigious trophy on 14 different times.
The Parisian giants needed a stoppage-time equaliser followed by a successful penalty shootout to overcome their arch-rivals in the Gulf and secure a fourth straight Trophee des Champions title.
The European champions appeared to be coasting towards a comfortable win in the showdown featuring the Ligue 1 winners and the Coupe de France holders after Ousmane Dembele found the scoring in the opening stages.
However, Marseille struck two times in the closing moments to take a shock lead. First, Mason Greenwood scored from the penalty spot, before the defender inadvertently directed the ball into his own net for an own-goal.
In a remarkable twist of events, the Portuguese striker snatched a vital leveler in the final moments to force the match into a deciding shootout. PSG goalkeeper Chevalier then emerged as the hero, saving decisive kicks from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, the midfielder, the full-back, and Desire Doue all scored successfully for Paris Saint-Germain to complete a convincing shootout victory.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now won this competition for the 12th time in the last 13 years.