PSG has now won the season-opening trophy on fourteen separate times.
The Parisian giants needed a stoppage-time equaliser followed by a successful spot-kick decider to get past their arch-rivals in the Gulf and capture a record-extending fourth consecutive French Super Cup title.
The European champions seemed to be coasting towards a comfortable win in the showdown between the Ligue 1 winners and the French Cup holders after Ousmane Dembele opened the scoring early on.
However, Marseille struck two times in the closing moments to take a shock lead. First, the English forward 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 vital equaliser in the dying seconds to send the contest into a penalty shootout. PSG goalkeeper Chevalier then emerged as the hero, stopping crucial kicks from Matt O'Riley and Traore.
From the spot, Ramos, Vitinha, Nuno Mendes, and the young talent all scored successfully for PSG to complete a convincing penalty victory.
The record champions PSG, who faced last season's Ligue 1 second-placed team Marseille after completing a domestic double, have now won this competition for the 12th time in the past thirteen seasons.