PSG won the trophy for a 16th time last season but lost to their newly promoted city rivals despite dominating the game.
Jonathan Ikone, who started his career with PSG, scored the only goal of the game after a perfectly timed run on the break.
Luis Enrique's side dominated but FC goalkeeper Obed Nkambadio made several fine saves, including an injury-time stop from a long-range Vitinha strike.
It was PSG's first last-32 defeat since 2014.
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