PSG has now won the prestigious trophy on 14 separate occasions.
The Parisian giants needed a dramatic equaliser followed by a perfect penalty shootout to get past their arch-rivals in Kuwait and capture a record-extending fourth consecutive French Super Cup victory.
The Champions League holders appeared to be coasting towards a straightforward triumph in the showdown between the Ligue 1 winners and the Coupe de France winners after the French winger found the net in the opening stages.
However, Marseille struck two times late to take a surprise advantage. Initially, the English forward scored from the spot-kick, before the defender inadvertently turned 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 dying seconds to force the contest into a deciding shootout. PSG goalkeeper Chevalier then emerged as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
In the shootout, Goncalo Ramos, Vitinha, Nuno Mendes, and the young talent all converted with composure for Paris Saint-Germain to complete a 4-1 penalty win.
The record winners PSG, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a league and cup double, have now won this competition for the twelfth time in the last 13 seasons.