Ayatullah Mazaheri was born into a religious family in 1934 in the city of Isfahan, Iran. He began his Islamic studies in the Hawza 'Ilmiyyah of Isfahan and completed his Arabic studies under the guidance of the late Hajj Agha Ahmad Muqaddas. His higher studies were conducted under the guidance of Ayatullah Khadimi, and Ayatullah Fayyad. Four years later, he moved to Qum to continue his studies under the supervision of the late scholar Shaikh Abd al‑Jawad Jabal al‑Amuli, the late Marja Ayatullah al‑Sayyid Shahab al‑Din Mar'ashi Najafi, and the late Ayatullah Shaikh Murtada Haeri.
For more than eight years, he studied Dars‑e‑Kharij under Ayatullah al‑Sayyid Husain Burujerdi, and then ten years under Ayatullah al‑Sayyid Ruhullah Musawi Khumayni, and twelve years under Ayatullah al‑Sayyid Muhammad Muhaqqiq Damad. He also studied the Al‑Asfar of Mullah Sadra and Al‑Shifa of Abu 'Ali Sind under the late Allamah al‑Sayyid Muhammad Husain Taba'taba'i.
Since 1980, he has been teaching the higher classes of Fiqh and `Usul, and he recently moved back to Isfahan to take over the responsibility of maintaining the Hawza `Ihniyyah there.