PSG has now claimed the season-opening cup on 14 separate times.
The Parisian giants needed a stoppage-time equaliser followed by a perfect penalty shootout to get past their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The European champions seemed to be coasting towards a straightforward triumph in the match featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the net early on.
Yet, Marseille fired two times late to seize a shock advantage. First, Mason Greenwood scored from the penalty spot, before the defender unfortunately turned the ball into his own net for an own goal.
In a breathtaking turn of fortune, Goncalo Ramos snatched a crucial equaliser in the final seconds to send the contest into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the key figure, stopping crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for PSG to complete a 4-1 penalty victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a domestic double, have now won this trophy for the twelfth time in the past 13 seasons.