The Parisian club has now won the season-opening trophy 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 record-extending fourth consecutive Trophee des Champions victory.
The Champions League holders appeared to be coasting towards a straightforward win in the match between the Ligue 1 champions and the Coupe de France holders 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 Willian Pacho unfortunately turned the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a crucial equaliser in the final seconds to send the contest into a deciding shootout. The Parisian shot-stopper Lucas Chevalier then emerged as the key figure, stopping crucial attempts from O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and the young talent all converted successfully for Paris Saint-Germain to complete a 4-1 penalty win.
Now 14-time champions Paris Saint-Germain, who met last season's Ligue 1 runners-up Olympique de Marseille after achieving a domestic double, have now won this trophy for the twelfth time in the last 13 seasons.