PSG has now won the season-opening trophy on fourteen separate times.
The Parisian giants needed a dramatic leveler followed by a successful spot-kick decider to overcome their arch-rivals in Kuwait and secure a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be sailing towards a comfortable triumph in the showdown between the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the net early on.
Yet, Marseille struck twice late to seize a surprise advantage. First, the English forward converted from the penalty spot, before the defender inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of events, Goncalo Ramos snatched a vital leveler in the dying seconds to force the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then emerged as the key figure, stopping crucial kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored successfully for PSG to seal a convincing penalty win.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now lifted this trophy for the 12th time in the past 13 seasons.