The third round of the evacuation was conducted under a Russia-backed deal between the Syrian regime and opposition. Elsewhere the SDF continued to advance on Tabqa dam and Raqqa.
A third group of opposition fighters and their families have left the last militant bastion in Syria's western city of Homs under an agreement with the Syrian regime that began in March.
Around 2,000 people boarded buses on Saturday heading to Syria's northwestern Idlib city, the UK-based Syrian Observatory for Human Rights (SOHR) said.
Al Waer, an early centre of the 2011 uprising against regime leader Bashar al Assad, has been under siege by regime forces since 2013.
The weekend's evacuation was conducted under a Russia-backed deal reached between the Syrian opposition and the regime on March 13 to transfer opposition fighters to Idlib or to other opposition-held areas near Aleppo city.
Under the evacuation deal, at least 12,000 people will be transferred to Aleppo province; 6,200 to Idlib; and 2,400 to Homs.
US-backed rebels repel Daesh attack on Tabqa dam
US-backed Syrian Democratic Forces (SDF) repelled a counter-attack by Daesh holding out at the country's largest dam and in the nearby town of Tabqa, the SDF and activists said on Sunday.
The dam is a key strategic target in the military campaign to isolate and capture the Syrian city of Raqqa, 40 kilometres (25 miles) to the east and Daesh's de facto Syrian capital.
An SDF spokeswoman said Daesh was stepping up resistance as SDF forces got closer to encircling the town and the dam.
The SDF is dominated by the YPG, which Turkey considers a terrorist group. It began an assault to capture the dam and the nearby town almost two weeks ago after the coalition landed some of its fighters on the southern side of the Euphrates near Tabqa, leading to its capture of an air base.
Daesh and the Syrian regime say the hydroelectric dam is vulnerable to collapse after coalition strikes.
Regime officials say that would lead to catastrophic flooding in the cities and towns in the Euphrates valley downstream.
The SDF and the coalition have denied the dam is in danger.
Residents, however, say an SDF attempt last week to relieve the dam's water levels by opening a canal from the Balikh River that flows into the Euphrates had flooded cultivated agricultural land in several villages.
Hundreds of families continued on Sunday to flee from villages under Daesh control.
The US-backed SDF says at least 7,000 people have taken shelter in areas under rebel control since the campaign to capture Tabqa began.
Many are also fleeing air strikes on civilian areas in Raqqa province that have left dozens dead according to activists and the Britain-based Syrian Observatory for Human Rights.
Last month strikes believed to be conducted by the US-led coalition hit a bakery and a local market in Tabqa town with dozens of civilians killed. Another raid that hit a school sheltering displaced people near Raqqa also killed scores.
SDF denies civilians are targeted.
Air strikes on Aleppo
Air strikes reportedly killed at least one fighter and wounded several people in northwestern Syria near a major border crossing with Turkey, two rebel sources said on Sunday.
Russian-backed regime forces carried out several raids in Babeska, a village in opposition-held Idlib province.
War jets believed to be Russian hit Urum al Kubra town in the rebel-held countryside of western Aleppo and killed five civilians.