PSG has now claimed the season-opening trophy on fourteen different times.
Paris Saint-Germain needed a stoppage-time equaliser followed by a perfect spot-kick decider to get past their arch-rivals in the Gulf and capture a fourth straight French Super Cup victory.
The Champions League holders seemed to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup holders after Ousmane Dembele found the scoring in the opening stages.
Yet, Marseille struck two times late to take a shock lead. Initially, the English forward converted from the penalty spot, before the defender unfortunately directed the ball into his own net for an own goal.
In a remarkable twist of fortune, Goncalo Ramos snatched a crucial equaliser in the dying seconds to send the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the key figure, saving crucial attempts from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and the young talent all converted with composure for PSG to seal a convincing shootout victory.
The record winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the 12th time in the past 13 years.