The Parisian club has now won the season-opening trophy on 14 separate occasions.
The Parisian giants required a stoppage-time leveler followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight Trophee des Champions title.
The European champions seemed to be sailing towards a straightforward triumph in the match between the Ligue 1 champions and the French Cup winners after Ousmane Dembele opened the net early on.
However, Marseille fired twice in the closing moments to take a shock advantage. First, the English forward scored from the spot-kick, before the defender unfortunately turned the ball into his own net for an own-goal.
In a remarkable turn of fortune, Goncalo Ramos snatched a vital equaliser in the dying moments to send the match into a deciding shootout. PSG goalkeeper Chevalier then emerged as the hero, saving crucial attempts from Matt O'Riley and Traore.
From the spot, Ramos, the midfielder, the full-back, and the young talent all scored with composure for PSG to complete a 4-1 penalty win.
Now 14-time winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after achieving a league and cup double, have now lifted this competition for the twelfth time in the last 13 years.