The court's decision upholds an earlier government decision. However, Kyrgyzstan's prosecutor-general, Kambaraly Kongantiev, could grant the two asylum based on an earlier decision by the UN High Commissioner for Human Rights to grant them refugee status.
The head of the UN refugee agency's mission in Kyrgyzstan, Carlos Zaccagnini, says he will urge Bishkek not to extradite the two men, Jakhongir Maksudov and Odiljan Rakhimov.
The two are wanted by Uzbek authorities on suspicion of involvement in what they view as a militant uprising in the city of Andijon in May 2005.
Maksudov and Rakhimov believe they may face persecution and torture if forced back into Uzbekistan, an assertion backed by human rights advocates.
Two other Uzbek nationals are awaiting similar court appearances. The Kyrgyz authorities have not yet said when those hearings will be held.