PSG has now won the season-opening trophy on fourteen separate times.
Paris Saint-Germain needed a dramatic equaliser followed by a perfect spot-kick decider to overcome their arch-rivals in the Gulf and secure a fourth straight French Super Cup victory.
The Champions League holders appeared to be sailing towards a straightforward triumph in the match featuring the French league winners and the French Cup winners after the French winger found the net in the opening stages.
Yet, Marseille struck twice late to take a shock advantage. First, the English forward scored from the penalty spot, before Willian Pacho inadvertently turned the ball into his own net for an own goal.
In a remarkable turn of events, the Portuguese striker grabbed a crucial leveler in the final seconds to send the match into a penalty shootout. PSG goalkeeper Lucas Chevalier then emerged as the hero, saving crucial attempts from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, the midfielder, Nuno Mendes, and Desire Doue all scored with composure for Paris Saint-Germain to complete a 4-1 penalty victory.
The record winners Paris Saint-Germain, who met last season's Ligue 1 runners-up Marseille after completing a domestic double, have now lifted this trophy for the twelfth time in the past 13 years.