The Parisian club has now secured the prestigious trophy on 14 separate times.
The Parisian giants needed a dramatic equaliser followed by a perfect penalty shootout to overcome their arch-rivals in the Gulf and capture a fourth straight French Super Cup title.
The Champions League holders seemed to be sailing towards a straightforward triumph in the showdown featuring the Ligue 1 winners and the French Cup winners after Ousmane Dembele found the scoring in the opening stages.
However, the southern French side struck two times in the closing moments to seize a shock advantage. First, Mason Greenwood converted from the spot-kick, 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 final seconds to send the match into a penalty shootout. The Parisian shot-stopper Lucas Chevalier then stood as the hero, saving decisive attempts from Matt O'Riley and Hamed Traore.
In the shootout, Ramos, Vitinha, Nuno Mendes, and Desire Doue all scored with composure for Paris Saint-Germain to complete a 4-1 penalty victory.
The record champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after completing a league and cup double, have now lifted this competition for the twelfth time in the last 13 years.
