Assad's forces and their allies punched their way into the city in September, breaking a almost three-year siege on the handful of neighborhoods that had remained under government control since the militants swept across large parts of Syria and Iraq in 2014.
Iraqi forces on Friday said they had begun their own final offensive against ISIS on the Iraqi side of the jihadist territory that straddles the border between the two countries, entering the city of al-Qaim.
Meanwhile the Syrian government, which is backed by Russian Federation has regained complete control of the eastern city of Deir al-Zor on Friday, representing a huge blow to the jihadists as their last stronghold in Syria crumbles.
Last month, USA -backed militias declared victory in Raqqa, Islamic State's former headquarters in Syria, after months of fighting for the city with the help of the US -led coalition.
Home to around 150,000 people, it is the last Iraqi remnant of ISIS.
He estimated there were 1,500-2,500 fighters left in al-Qaim and 2,000-3,000 in Albu Kamal.
Syrian government forces and their pro-government allies first broke the militant group's siege of their part of the city in September in a Russian-backed offensive, and have been advancing against IS positions since then.
The commander added that Iraqi forces have also established control over the nearby Al-Qaim border crossing.
Troops from the army and the elite Counter Terrorism Service "have started the assault on the center of Al-Qaim", Staff Major General Noman Abed al-Zobai, the commander of the 7th Division, told AFP from the scene.
Deir Ezzor had been divided into government-held and ISIS-held parts for almost three years.
"Iraqi security forces have fought hard to reach this point, and their battle-proven troops captured ISIS's last Iraqi stronghold swiftly and thoroughly", said Army Maj.