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.
"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.
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.
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