Ayatollah Sadeq Larijani has appointed Abbas Jafari Dolat-Abadi as Tehran prosecutor for public and revolutionary courts, the official IRNA news agency reported. It did not explain the reason for the Mortazavi's removal.
Jafari Dolat-Abadi was the justice chief in the western province of Khuzestan.
Mortazavi, 42, was a judge before his appointment as Tehran prosecutor in 2003. "He shut down 120 publications in his time," the reformist Sarmayeh newspaper said.
Larijani was named judiciary chief earlier this month as Iran grappled with its worst crisis since the 1979 Islamic revolution following the massive protests against the disputed re-election of President Mahmoud Ahmadinejad.
About 4,000 people were initially arrested and Mortazavi has put on trial 140, including senior reformers, journalists, a French woman lecturer, and two local staff at the British and French embassies.
The defendants are accused of seeking a soft overthrow of the regime and inciting "riots" but the opposition has condemned the "show trials" and alleged that detainees have been raped, tortured and coerced into confessions.
Canada has also called for Mortazavi's prosecution over the death of Iranian-Canadian journalist Zahra Kazemi, who died in July 2003 after spending two weeks in custody in Tehran.
Larijani has also appointed a new panel to oversee cases linked to the violent election aftermath such as reported attacks on university dormitories and the closure of a jail amid claims of prisoner abuse.
"It is required that you consistently pursue and oversee the proceedings, identify offenders and main elements and firmly confront them regardless of their ranks," the judiciary chief told the panel according to IRNA.
