Reporters saw scores of militants and their families leaving the area on Saturday in buses bound for the northern rebel-held town of Jarablous on the border with Turkey, the New Arab reported.
Known as "reconciliation agreements," this is one of the Syrian government's local pacts that allow surrendering civilians and fighters to evacuate to other rebel-held regions.
The initiatives are designed to help put an end to the country's long-running war and reestablish stability in what were war zones.
The Syrian Arab Red Crescent, along with Russian and Syrian authorities, are supervising the Al-Waer evacuation.
The Syrian Army has wrestled back complete control of Homs city in the previous months – with the exception of al-Waer – and last year announced plans for rebuilding projects in several districts of the city.
Syria has been gripped by militancy it blames on some Western states and their regional allies since March 2011.
According to independent monitors, hundreds of thousands of civilians have been killed in the war and millions have been displaced both inside and outside of Syria.