'Islamic State has fallen' says top Iraqi commander
"Their fictitious state has fallen," Iraqi military spokesman, Brigadier General Yahya Rasool, told state TV.
In 2014, IS leader Abu Bakr al-Baghdadi declared a "caliphate" from the historic Mosul mosque.
"Counter-Terrorism Service forces control the Nuri mosque and al-Hadba (minaret)", the Iraqi Joint Operations Command said in a statement.
Baghdadi made his first and only public appearance at the mosque during Friday prayers in 2014, but three years later his fate is unknown and IS has lost most of the territory it overran that year.
The Battle for Mosul began over eight months ago and IS has been making a last stand in the historic Old City.
The militant group blew up the Grand al-Nuri mosque on 21 June in increasingly desperate resistance to the advance of Iraqi forces, with Iraqi Prime Minister Haider al-Abadi declaring it an "official declaration of defeat".
The loss of the iconic 12th century minaret - one of the country's most recognisable monuments sometimes referred to as Iraq's Tower of Pisa - left Iraqis shocked.
IS claimed on its Amaq propaganda agency that the site was hit in a US air strike, but the US-led coalition said it was the group who had destroyed the historic religious building.