Much of the southern province of Daraa had been quiet since Friday, when a cease-fire deal between rebels and the Russian-backed regime ended a almost three-week government assault.
Dara'a city was the birthplace of the sedition that began in March 2011 before morphing into a foreign-backed militancy that continues to this day.
The Syrian Observatory for Human Rights, which has been monitoring the war, said rebels were still in the city, but on Thursday their departure appeared to be merely a matter of time.
Zaizun lies near a sliver of southern territory controlled by Jaish Khaled bin Walid, a jihadist faction that has pledged allegiance to IS, which is not bound by the deal between the rebels and the government.
"It is a strategic and a symbolic win for the Syrian government".
Syrian forces are seen in the Nasib border crossing with Jordan in Dara'a, Syria, July 7, 2018. The talks were expected to resume on Thursday.
Rebels quickly sought to negotiate with Assad's Russian sponsors after the USA, which for years had backed the southern rebels, said it would not intervene militarily to protect them.
Latest estimates say some 2,000 militants are still holed up in Dara'a city, along with their families.
"Units of the Syrian Arab army entered the district of Daraa al-Balad and raised the national flag in the main square ... a declaration that Daraa is now clear of terrorism", said the state news agency Sana, referring to the opposition groups as terrorists.
The current progress comes after controlling all the borders with Jordan, the report said, adding that the Syrian regime helicopters dropped warning leaflets on Al-Hara village in the northwestern Daraa countryside where the highest hill in the city is located.
"At least 27 regime forces and allied fighters, including eight officers, were killed in fierce clashes and shelling in the village of Al-Ateira", said Observatory head Rami Abdel Rahman.