Frenchman Haise has signed a contract until 2027 after Beye was dismissed with the Breton outfit sitting in sixth place in Ligue 1.
Beye has been heavily linked with the vacant Marseille job, but a move to the Stade Velodrome is on hold due to discussions over his severance package with Rennes.
Haise, 54, guided Lens to the Champions League group stage in 2023/24 after the club finished runners-up in Ligue 1 the previous season. He joined Nice in June 2024 but left last December after just five wins from 16 league games. Haise returns to Brittany after a six-year stint as a coach in the Rennes academy from 2006-12.
Haise's first game in charge will be Sunday's trip to struggling Auxerre. Rennes stunned Paris Saint-Germain 3-1 last Friday and are on course for a spot in next season's Europa League.