The Parisian club has now claimed the season-opening cup on 14 different occasions.
Paris Saint-Germain required a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in Kuwait and capture a fourth straight French Super Cup title.
The European champions appeared to be coasting towards a straightforward win in the match between the Ligue 1 winners and the Coupe de France winners after the French winger found the net early on.
However, Marseille struck two times late to seize a shock advantage. First, the English forward scored from the penalty spot, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable twist of events, the Portuguese striker grabbed a vital equaliser in the final seconds to force the match into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, saving decisive attempts from O'Riley and Traore.
From the spot, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for Paris Saint-Germain to seal a 4-1 shootout victory.
Now 14-time winners PSG, who faced last season's Ligue 1 second-placed team Olympique de Marseille after completing a league and cup double, have now won this trophy for the 12th time in the last thirteen years.
