The Russian-supervised evacuation of the Waer district was the latest blow to the insurgents by regime troops backed by their Russian and Iranian allies.
Since December, the rebels have lost their former bastion of Aleppo and nearly all of the areas they controlled in Damascus.
This latest setback is mostly symbolic, however, as most of the rebels had been driven out of Homs in 2014 after two years of bombardment and stifling siege.
"The last bus (with evacuees on board) has left the Waer neighbourhood," Homs provincial governor Talal Barazi told AFP.
On Saturday, he had said that 3,000 evacuees, including 700 rebels, were due to be taken out of Waer.
"There are no more weapons or armed men in Waer... we can declare Homs to be a secure city," Barazi said, referring to the rebels.
He added that the Syrian security services had now entered the former rebel bastion.
An AFP correspondent said the evacuees left on board 50 buses as more than 30 trucks packed with household belongings trailed behind.
Many rebels wore black scarves to conceal their faces, some holding light weapons authorised under the deal while families lugged suitcases and children carried toys.
"I feel like I am dying inside. I wanted to stay but I was afraid of being arrested," one rebel, who shielded his eyes behind sunglasses, told AFP.
The Russian-supervised operation began two months ago and has been carried out over several weeks.
Under the deal, opposition fighters are granted safe passage by the government out of Homs to rebel-held areas elsewhere in Syria, including the northwestern Idlib province.
Between 600 and 100 Russian soldiers will deploy in Waer to provide security for residents who still live there or for those who were displaced by fighting and wish to return home.
The evacuation of Waer will bring Syria's government closer to cementing its control over more parts of the war-wracked country.
Earlier this month, rebels also began evacuating the last districts under their control in the capital Damascus, following their defeat in second city Aleppo in December.