Counter terrorism units have taken control of the centre of the city, which includes its historic Ottoman citadel.
"They raised the Iraqi flag on the citadel," General Abdulamir Yarallah, commander of military operations in the battle for Tal Afar, said in a statement.
The advance, less than a week into an assault on the strategic city, comes after Prime Minister Haider al-Abadi declared victory in July over the fighters in Iraq's second city Mosul, where ISIS declared its "caliphate" in 2014.
Iraqi forces now hold "94 percent of the city, 27 out of 29" districts including the centre and citadel, according to the Joint Operations Command (JOC) which coordinates the anti-ISIS operation in Iraq.
The announcement Saturday came as the French foreign and defence ministers visited Baghdad to announce a loan of 430 million euros ($512 million) to help the Iraqi economy in the face of low oil prices and the cost of battling the ISIS fighters.
On Saturday, units also battled ISIS around Al-Ayadieh, 15 kilometres (10 miles) north of Tal Afar and strategically located on the road between the city and the Syrian border, Yarallah said.
In the whole Tal Afar region, "1,155 square kilometres of 1,655 square kilometres, or 70 percent of the area, have been taken" the JOC said.
Columns of smoke could be seen rising over the city after the Hashed al-Shaabi paramilitary coalition fighting alongside government troops seized the Al-Khadra and Al-Jazeera districts.
Abbas Radhi, a Hashed al-Shaabi fighter, said ISIS had resisted the advance mostly with sniper fire.
"There are also booby-trapped cars, mortars. But they've been defeated, God willing," he said.
Government troops and units of the Hashed al-Shaabi, backed by a US-led coalition against ISIS, launched the assault last Sunday after weeks of coalition and Iraqi air strikes.
Tal Afar sits on a strategic route between ISIS-controlled territories in Syria and Mosul, 70 kilometres (40 miles) further east.
Progress in Tal Afar has been far more rapid than in Mosul, which fell to Iraqi forces only after a gruelling nine-month battle.
Officials have said they hope to announce victory by Eid al-Adha, the Muslim holiday set to start in Iraq on September 2.
Until its takeover by ISIS, Tal Afar was largely populated by Shiite Turkmen, whose beliefs are anathema to the Sunni jihadists.
Some members of Tal Afar's Sunni minority joined jihadist ranks, forming an ISIS contingent with a particular reputation for violence.
Pro-government forces faced an obstacle course of roads blocked with earth embankments and strategically parked trucks, as well as sniper fire and mortar shelling.
Troops also said they discovered a network of underground tunnels used by ISIS to launch attacks behind lines of already conquered territory, or to escape.
Officials have said the capture of the city would make it even more difficult for the jihadists to transport fighters and weapons between Iraq and Syria.
The jihadist group has lost much of the territory it controlled and thousands of its fighters have been killed since late 2014, when a US-led international coalition was set up to defeat the group.
Iraq announced the "liberation" of Tikrit, 160 kilometres (100 miles) north of Baghdad, in early 2015.
The ISIS group's biggest defeat was in Mosul, where some 30,000 Iraqi forces backed by US-led air support launched a vast operation in October.
Three months later, they retook the Mosul's east and turned their attention to the west, finally declaring the whole city "liberated" on July 9.
The ISIS still retains territory in Iraq and neighbouring Syria, where a US-backed Kurdish-Arab coalition is fighting to drive the group from its de facto Syrian capital Raqa.
Once Tal Afar is retaken, Baghdad is expected to launch a new offensive on Hawija, 300 kilometres north of Baghdad.
ISIS is also present in the vast western province of Anbar, where it controls several zones along the border with Syria, including the Al-Qaim area.
The Tal Afar advance came as the foreign and defence ministers of France visited Baghdad to reaffirm their country's support in the fight against ISIS.
France is to extend the loan of 430 million euros before the end of 2017, Foreign Minister Jean-Yves Le Drian said in a meeting with Abadi.
"As long as our common enemy has not been eradicated, France will continue to take part" in the campaign, said Defence Minister Florence Parly, whose country's forces have carried out air and artillery strikes in support of Iraqi operations.