PSG has now secured the season-opening cup on 14 different occasions.
The Parisian giants needed a dramatic leveler followed by a perfect spot-kick decider to overcome Marseille in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The Champions League holders appeared to be sailing towards a straightforward win in the showdown featuring the Ligue 1 champions and the Coupe de France holders after the French winger found the scoring early on.
Yet, Marseille fired twice in the closing moments to seize a surprise lead. First, the English forward scored from the spot-kick, before the defender inadvertently directed the ball into his own net for an own goal.
In a remarkable turn of fortune, the Portuguese striker grabbed a vital leveler in the final seconds to send the contest into a deciding shootout. PSG goalkeeper Lucas Chevalier then stood as the key figure, saving decisive kicks from Matt O'Riley and Hamed Traore.
From the spot, Goncalo Ramos, Vitinha, the full-back, and Desire Doue all scored with composure for PSG to seal a convincing shootout victory.
The record winners Paris Saint-Germain, who faced last season's Ligue 1 second-placed team Marseille after completing a league and cup double, have now won this competition for the 12th time in the past 13 years.