When he was handed over to the C.I.A. rendition team at the Skopje airport, he was “severely beaten, sodomized, shackled and hooded” in the presence of Macedonian officials, the ruling said, a treatment that “amounted to torture.” He was then flown to Afghanistan, where he spent more than four months in captivity before being flown to Albania and dropped on the side of a road.

His German lawyer, Manfred Gnjidic, said his mental state had suffered not only from the abuse but also from the “nine years of constantly fighting, being called a liar, a terrorist, an Islamist, a hard-liner.” Mr. Masri has broken off contact with his lawyers while serving a prison sentence on unrelated charges involving a 2009 assault on the mayor of Neu-Ulm in Bavaria.

Mr. Gnjidic said he had written to Chancellor Angela Merkel of Germany asking the government to appeal to Washington on Mr. Masri’s behalf. “Macedonia was only the henchman of the great powers,” Mr. Gnjidic said. “The question is: What is with the big fish, with Germany, with the U.S.A.? All he ever wanted was to know why this was done to him and an apology.”

Jamil Dakwar, the head of the A.C.L.U.’s human rights program, said that it had been “an uphill battle” to persuade the Obama administration to hold officials accountable under international law for Mr. Masri’s mistreatment, but that the case before the commission “gives the Obama administration the opportunity to acknowledge the egregious violations against Khaled, offer an official apology and reparation.” He called the European court’s ruling “historic” and said it “sends the message to European nations that they have a heightened obligation to investigate their complicity and cooperation with the illegal C.I.A. extraordinary rendition program.”