Stimac takes charge of the Isfahan-based team until the end of the season.
Sepahan parted company with Hossein Faraki on November 1 by mutual consent.
Iran Professional League title-holder Sepahan currently is sixth in the table, five points behind leader Esteghlal.
Stimac had been widely expected to be named as Esteghlal coach in summer but the Iranian popular team appointed Parviz Mazloumi as the head coach.