It was the latest in a string of reverses for IS in Syria this month that on Tuesday saw US-backed forces capture its emblematic bastion Raqa.
The jihadists had seized Al-Qaryatain on October 1 in a surprise counteroffensive against the Homs province town which they had lost to Russian-backed government forces in April last year.
"Units of the Syrian Arab Army in cooperation with allied forces have restored security and stability in the town of Al- Qaryatain after eliminating the Daesh terrorists," the state SANA news agency reported, using an Arabic acronym for IS.
There was no immediate word on the fate of the town's residents during IS's three-week reoccupation.
Al-Qaryatain was a symbol of religious coexistence before the civil war broke out in 2011, with some 900 Christians among its population of 30,000.
But during their first eight-month-long occupation of the town in 2015-16, the Sunni Muslim extremists of IS repeatedly targeted its Christian minority.
The jihadists also destroyed parts of a monastery in the town and reduced a fifth-century mud brick church to rubble using explosives and bulldozers.
Government forces are engaged in twin Russian-backed offensives against IS, mopping up the last pockets it still holds in the desert and pushing down the Euphrates Valley towards the Iraqi border in the east.
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