Uzbek foreign ministry spokesman Yusup Kabulzhanov confirmed the evacuation by saying that "All Afghan refugees have left the territory of Uzbekistan.
The United States has said it evacuated nearly 500 "military and civilian" Afghans from Uzbekistan, while the ex-Soviet country declared there were now no Afghan refugees on its territory.
The days leading up to the Taliban's capture of Kabul caused scenes of chaos in Afghanistan's Central Asian neighbours Uzbekistan and Tajikistan, as soldiers loyal to the crumbling government fled over state borders in military aircraft.
Uzbekistan had mostly withheld comment on the number and status of the refugees as it looked to cultivate ties with the Taliban next door.
But a US embassy spokesman told AFP on Tuesday it had evacuated 494 "military and civilian" Afghans out of Uzbekistan's southern Termez airport with the Uzbek government's help.
"The evacuation was completed September 12-13," the spokesman told AFP by telephone, making no comment on the final destination of the refugees.
Uzbek foreign ministry spokesman Yusup Kabulzhanov on Monday confirmed the evacuation in comments to a privately-owned news outlet.
"All Afghan refugees have left the territory of Uzbekistan,” he said, without giving figures.
A staffer at Afghanistan's embassy told AFP last month that up to 1,500 Afghans might have crossed into Uzbekistan illegally after the Taliban secured control of the northern stronghold Mazar-i-Sharif in mid-August and began beating a path towards Kabul.
In a rare statement on the refugees in August, Uzbekistan said it had returned 150 people to Afghanistan at their own request and following talks with the Taliban to guarantee their safety.
Thousands of Afghans in Tajikistan
Tajikistan, which has eschewed official contacts with the Taliban, has been similarly secretive about the number of refugees it has taken in.
The European Union's delegation in the country said on Tuesday that it was providing 160,000 Euros in humanitarian aid funding "to benefit up to 5,000 displaced Afghans" in two Tajik provinces bordering Afghanistan.
The EU statement cited the UN Refugee Agency (UNHCR) as saying that "up to 50,000 refugees could be registered in Tajikistan after the total withdrawal of American and NATO troops by the end of 2021.”
The statement comes after Interior Minister Ramazon Hamro Rahimzoda earlier this month criticised international donors for failing to help Tajikistan house refugees.
Afghanistan is set to dominate discussions at the summit of the Shanghai Cooperation Organisation, a bloc that includes four ex-Soviet Central Asian countries, China, India, Pakistan and Russia, hosted by Tajikistan this week.