This was the second major evacuation in Syria this past week.
On Thursday, buses removed more than 6,000 people from two Shiite villages in Idlib Province in the north who had been besieged by Sunni rebels for years.
Idlib now holds the largest patch of rebel-held territory in Syria, and officials in the region assume that once Mr. Assad has retaken the south, he will turn his guns to Idlib.
More than two million people are there, many displaced from elsewhere in Syria, and aid organizations worry that any military operation would be catastrophic because civilians will have nowhere to flee. The province borders Turkey, which has kept its border closed.
The two Shiite villages, which contained civilians and fighters loyal to the Syrian government, had been under siege by rebel forces for years. Last week, a deal was reached for them to be emptied out and their residents bused to government-held areas farther south in exchange for the release of about 1,500 detainees held by the government.
The departure was bitter for those who left, not knowing if they would ever return.
“We were hoping for a military campaign to reach us here, but unfortunately nothing happened and we’re leaving,” Hussein Halaq, a Shiite villager, said via a messaging app as he prepared to leave. “Many lost their houses and their future.”
But some who remained in Idlib worried that the departure of the Shiites was the government’s way of paving the way for a harsh military attack, since it no longer had to worry about collateral damage to its loyalists.
“They were like a card for us, pressing the regime warplanes not to bomb civilians,” said Mohammed Saeed, an antigovernment activist in Idlib.