The last rebels were leaving the centre of the battleground city of Homs, handing a symbolic victory to Syrian President Bashar al-Assad ahead of a controversial election.
Rebels hit back in the historic heart of Aleppo, blowing up a luxury hotel-turned-army position after tunnelling under the front line which divides the main city of northern Syria.
At least 14 soldiers and pro-government militiamen were killed in the explosion and its aftermath on Thursday, the Syrian Observatory for Human Rights said.
Around 1,000 rebel fighters have left the Old City of Homs under the unprecedented negotiated evacuation that began on Wednesday, according to figures given to AFP by provincial governor Talal Barazi.
But seven buses carrying the last 300 fighters were stopped because Islamist fighters were refusing to allow food supplies into two rebel-besieged Shiite towns in Aleppo province, the Observatory said.
Barazi said they were stopped at the northern exit from the Old City, without giving a reason.
Rami Abdel Rahman, who heads the Syrian Observatory, said Islamists were limiting entry of supplies to Zahraa and Nabol to two trucks, instead of 12 as agreed by the regime and rebels in negotiations to which they were not a party.
Barazi earlier said more than 200 fighters had been evacuated on Thursday in addition to 980 people, mostly rebels but including some women and children, bussed out of the Old City on Wednesday.
The pullout, following an army siege of nearly two years, leaves the rebels confined to a single district on the outskirts of a city that what was once a bastion of the uprising. Barazi said negotiations were well advanced for the rebels to leave that neighbourhood too in the coming weeks.
He said the fighters and some civilians evacuated with them were bussed out to the opposition-held town of Dar al-Kabira, 20 kilometres north of Homs.
Government troops played football on the square housing Homs’s landmark clock tower, once the scene of the city’s massive anti-government protests.
A soldier climbed onto the rooftop of a house and told AFP: “This is the first time I climb up here without fearing snipers.”
“Come on, shoot me!” he called out to another soldier, who took a photograph of him.
It is not the first deal between the government and the rebels – a number of ceasefires have been agreed on the outskirts of Damascus. But it is the first time that rebel fighters have withdrawn from an area they controlled under an accord with the government.
The Syrian government allowed the remaining rebels in Homs to pull out with their personal weapons in return for the release of 40 Alawite women and children, an Iranian woman and 30 soldiers held hostage by rebels elsewhere in Syria, a rebel spokesman said.
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