PSG has now secured the prestigious cup on fourteen different times.
The Parisian giants required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive Trophee des Champions victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the showdown between the Ligue 1 champions and the French Cup holders after the French winger opened the scoring in the opening stages.
Yet, Marseille struck two times in the closing moments to take a surprise lead. First, Mason Greenwood scored from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a breathtaking turn of fortune, Goncalo Ramos grabbed a vital leveler in the final moments to send the contest into a penalty shootout. The Parisian shot-stopper Chevalier then emerged as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored successfully for PSG to seal a 4-1 penalty win.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Marseille after completing a league and cup double, have now won this trophy for the twelfth time in the past thirteen years.