A suicide vehicle bombing on Tuesday killed 14 newly reconciled fighters from pro-government and rebel ranks in an attack on a south Syrian village claimed by the militant Islamic State group.
The mosque has since been destroyed in the government's brutal crackdown against the city, which ranged from alleged torturing of dissidents to shelling the city with tanks and planes.
An Islamic State group affiliate took control of Heet, near the Jordanian border, despite Russian and regime air strikes against them.
The corner of south-west Syria is an important corridor for trade between Syria and Jordan, and onward to the oil-rich Gulf states.
The fall of Daraa will remain the only substantial rebel-held territory will be in the far north, along the Turkish border.
Some 400,000 people have been killed in seven years of war.
Syrian state media said Assad's forces hoisted their flag for the first time in years in the rebel-controlled parts of the city after a surrender deal was agreed with local rebels, which included a planned handover of weapons and the exile of opposition fighters and activists.
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Much of the southern province of Daraa had been quiet since Friday, when a ceasefire deal between rebels and the Russian-backed regime ended a almost three-week regime assault.
The Damascus regime is bent on retaking the whole of Daraa province, including its symbolic capital where 2011 protests against President Bashar al-Assad are seen to have started the uprising that spiralled into civil war.
The Syrian regime and its ally Russian Federation had launched an all-out air assault on Ghouta in February to force antigovernment rebels to surrender.
Latest estimates say some 2,000 militants are still holed up in Dara'a city, along with their families.
A militant official said the Takfiri elements, who are still holed up in Dara'a, are in talks with Russian officers to secure a safe passage to the terrorist-controlled areas in northern Syria. Those who refuse to cooperate would be evacuated.
New combat footage released by ANNA news agency, showing the storming units of the Syrian Army marching on last rebel defenses in the southeastern countryside of Daraa.