A state television presenter said the recovery of al-Hajar al-Aswad meant the area south of Damascus had been completely cleared of insurgents.
A temporary humanitarian ceasefire had been in place since Sunday night in al-Hajar al-Aswad to allow women, children and old people to leave the area, state media said early on Monday (local time).
Thirty-two buses transported 1,600 people out of the areas on Sunday and Monday, and headed towards the Badiya region, a vast stretch of desert in south-eastern Syria where IS still controls pockets of territory, the monitoring group said.
A civilian convoy left the Yarmouk refugee camp near Damascus on Monday after a deal was struck to this effect between Syria's Assad regime and the Daesh terrorist group.
An Al-Ikhbariya reporter in the area said the coming hours will be "decisive" for restoring government control over Hajar Al-Aswad, but did not mention Yarmouk.
The Syrian army is clearing out the last remaining blocks of the recently liberated Yarmouk camp, located in the south of Damascus, a Sputnik correspondent reported.
It follows months of battles between ISIS fighters and Syrian government and allied troops in southern Damascus, leaving scores dead and leaving the already battered Yarmouk refugee camp an even greater scene of destruction.
Syria's war erupted in 2011 with protests against President Bashar al-Assad, including in the capital.
A military source close to the regime said the deal had been reached through negotiations with the government and its ally Russian Federation.
Takfiri militants have lost much of the territory they once held in Syria amid sweeping gains by government forces on the ground over the past few months.
Majority were former members of Al-Qaeda's Syrian ex-affiliate Al-Nusra Front, but IS fighters there also included Palestinian refugees who joined when the Islamists took over much of the camp in 2015.
Putin's envoy to Syria, Aleksandr Lavrentyev, said Putin was referring to, among others, Iranian forces.
While Assad has vowed to win back "every inch" of Syria, the map of the conflict suggests a more complicated time ahead from now on.
One spokesman for a Free Syrian Army (FSA) rebel faction in the Badia told Syria Direct on Monday that his forces had monitored the arrival of buses allegedly carrying Islamic State members.