The December 13 decision by the court in Strasbourg, France is the first major legal victory for Khaled el-Masri.
The Lebanese-born German citizen says he was abducted by the CIA in Macedonia in 2003.
El-Masri says the CIA kept him in a Skopje hotel for 23 days and then interrogated him at a secret prison in Afghanistan, where he remained until 2004.
Macedonia denied involvement in the kidnapping, but the court ordered Skopje to pay $78,300 in damages.
Previously, el-Masri brought unsuccessful legal cases in the United States and Europe against the practice of “extraordinary rendition” or the capture and extrajudicial transfer of suspects from one country to another.