Rights activists say as many as 750 people were killed by security forces in the 13 May confrontations in Andijan, mostly unarmed civilians demonstrating against poverty and political and religious oppression in the former Soviet republic.
Uzbek officials say 187 people died in the violence - half of them armed militants. It blamed the uprising on Islamic radicals.
The 439 refugees, including 23 children, 74 women and 342 men, waved and flashed peace signs with their hands at the airport in Timisoara in western Romania as they arrived on Friday.
The Uzbeks had taken refuge in neighbouring Kyrgyzstan in May.
The refugees will stay in a European Union-funded centre located in a former military barracks at the edge of Timisoara 500km (310 miles) west of Bucharest.
Reporters were not allowed access to the refugees. Veerapong Vongvarotai, the UN High Commissioner for Refugees' representative in Romania said the Uzbeks would be given medical care and food. He said several countries were
interested in helping them.
Vasile Dragoi, who heads the refugee centre in Timisoara, said the Uzbeks would stay in the centre where they "would be given protection".
Uzbek refugees flee to
Kyrgyzstan in May (File picture)
"They will not leave this centre, except for in exceptional situations such as medical emergencies or them leaving for the final destination countries," Dragoi said.
Foreign Minister Mihai Razvan Ungureanu said on Thursday the Uzbeks would remain in Romania for up to six months and then would be sent to other countries, including the United States, the Netherlands and Canada.
The asylum-seekers had been living at a UN-sponsored camp near the border with Uzbekistan.
Since then, Uzbekistan has been pressuring Kyrgyzstan to hand over the refugees, prompting the United Nations to make plans for moving the asylum-seekers to another country, fearing they could face persecution or torture if they are forced to return home.