Homs Governor Talal Barazi said "the city of Homs is completely clear of weapons and militants after completing the reconciliation deal in al-Waer district," Syrian state TV reported.
Government forces backed by the Russian military have already moved into many areas of al-Waer, state media say.
Some 700 fighters and their families, a total of nearly 3,000 people according to Barazi, left aboard buses on Saturday and Sunday in the final phase of the evacuation of insurgents from al-Waer. Government troops had long besieged the last opposition-held area in a city that was one of the early centers of the anti-Assad uprising.
Thousands of opposition fighters and their families have left a number of areas in western Syria in recent months in what the government calls reconciliation deals. Assad's government now controls the country's main urban centers.
The opposition and the United Nations have criticized the deals as forced displacement of Assad's enemies, often after months or years of siege and bombardment.
One of the rebels leaving al-Waer on Sunday said many of the fighters had come to the district from other areas of Homs, including the Old City, after those areas were retaken by government forces earlier in the conflict.
"I don't want to stay here. I'll go to Idlib, and want to go on to Turkey and then Europe after that," he said to a Reuters journalist on the scene before the buses left, without giving his name.
Evacuees have mostly headed for insurgent-held Idlib province, or for Jarablus, a town along Syria's northern border near Turkey.
Most leave, some stayAl-Waer has been under full siege for more than a year, according to the Britain-based Syrian Observatory for Human Rights monitoring group.
Government forces backed by Russian military police had begun to take control of key parts of the district, a Russian officer told Syrian state TV.
Moscow, a key Damascus ally, has helped Assad gain the upper hand against insurgents in the west of the country, along with the support of Iranian fighters and members of Lebanon's Hezbollah Shi'ite militia. Western nations, Gulf Arab states and Turkey support the opposition.
Barazi said that more than 14,000 people had left al-Waer in several phases since the agreement began to be implemented in March. Among them were some 3,700 rebels, allowed to leave with their light weapons.
State television early on Sunday showed rebels milling around, depositing bags and suitcases in front of buses, and holding Kalashnikov assault rifles as armed men from the government side watched the proceedings.
Some 1,150 rebel fighters have decided to stay in the district and hand over their weapons under a government amnesty, Barazi said.