PSG has now won the season-opening cup on fourteen different occasions.
The Parisian giants required a dramatic leveler followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders seemed to be sailing towards a comfortable triumph in the match featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele opened the net in the opening stages.
However, Marseille fired two times in the closing moments to seize a surprise lead. First, Mason Greenwood scored from the spot-kick, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a vital equaliser in the final seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping crucial kicks from Matt O'Riley and Traore.
In the shootout, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all converted with composure for PSG to seal a 4-1 shootout win.
The record winners PSG, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now lifted this trophy for the 12th time in the past 13 years.