Earlier the Syrian Observatory for Human Rights, a UK-based activist group, said government forces had taken control of the city after weeks of fighting.
The militant group is now confined to just a few pockets in Deir al-Zour province. Some 350,000 civilians in the province have been forced to flee their homes.
Last month a US-backed alliance of Syrian fighters pushed IS out of the eastern city of Raqqa, the headquarters of its self-styled “caliphate”.
The Syrian Democratic Forces (SDF) and Syrian government forces – which are backed by Russian air strikes and fighters from Lebanon’s Hezbollah movement – have been carrying out separate offensives in Deir al-Zour province with the aim of taking control of a key crossing on the border with Iraq.
In some areas the US-backed SDF and Russia-backed Syrian army have taken up positions just a few kilometres apart.
IS has also suffered a series of defeats in recent months to Iraqi government forces, who are advancing along the Euphrates river on the other side of the border.