The club confirmed in a tweet that Pochettino had returned a positive PCR test and will enter self-isolation.
Assistants Jesus Perez and Miguel D'Agostino will take charge for Saturday's clash at the Stade Jean-Bouin.
After a 1-1 draw against Saint-Etienne in his first game at the helm, Pochettino has overseen a 3-0 win over Brest and a 2-1 Trophee des Champions victory against Marseille.
Wednesday's defeat of PSG's arch rivals secured Pochettino's first trophy of his career as a coach. PSG are a point behind Lyon at the top of Ligue 1.