In a statement, the military said it was now in full control of the city, after a weeks-long campaign carried out with allied forces. It said army units were now removing booby traps and mines left behind by the extremist group in the city.
Deir el-Zour, on the west bank of the Euphrates River, had been divided into a government-held and an IS-held part for nearly three years.
The development is the latest significant defeat for IS as the militant group sees its self-proclaimed "caliphate" crumble and lose almost all urban strongholds, including Mosul in Iraq and Raqqa in northern Syria.
It also comes as Iraqi forces and allied Shiite militiamen are chasing IS remnants inside the town of Qaim, on the Iraqi side of the border.
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Moscow's military involvement in the Syrian war since 2015 has propped up President Bashar Assad's forces and turned the conflict in his favor, while Russian mediation earlier this year launched cease-fire talks in Astana, Kazakhstan.
The talks, sponsored jointly with Iran and Turkey, have brokered local deals that have significantly reduced violence in the war-torn country.
Footage posted on the website of the Syrian state news agency SANA shows the last moments of the fighting between the Syrian army and IS in Deir el-Zour, including shelling by Syrian tanks and plumes of smoke rising over the city's IS- held and mostly destroyed neighborhoods of Jamiayat and Jabiliyeh before they were liberated.