The panel on Thursday ruled that Turkey had violated Article 3 of the European Human Rights Convention regarding prohibition of inhuman and degrading treatment.
The prisoner Lazgin Biyan, was stripped and administered electric shocks and also beaten mercilessly while in police custody.
His interrogators were seeking to extract a confession from him about his links to Kurdish separatists.
"The court found that the prisoner had received his injuries as a result of his treatment in police custody," a press release of the Human Rights Court said.
"Noting that his injuries were consistent with ill-treatment amounting to inhuman and degrading treatment, the court held unanimously that there had been a violation of Article 3."
The Strasbourg-based tribunal also ruled that Turkey had violated Article 6 regarding the right to a fair trial, because the state security court which had tried and convicted the applicant was not impartial and independent.
The court awarded Biyan $11,650 in damages.
Biyan, 34, was arrested in 1997 on suspicion of membership of a secret committee providing assistance to the Kurdistan Workers' Party (PKK).
He was later sentenced to 12 years' imprisonment for membership of an illegal organisation.
The PKK waged a 15-year war for self-rule in the mainly Kurdish eastern and southeastern parts of Turkey - claiming more than 36,000 lives - before announcing a unilateral ceasefire in 1999.
It is on the EU's list of terrorist organisations.
In December, Turkey was invited by the EU to begin membership talks in October. But the country was advised that it must ensure that recent legislation adopted to improve human rights was applied at all levels.
The European Court of Human Rights was set up in Strasbourg by the Council of Europe Member States in 1959 to deal with alleged violations of the 1950 European Convention on Human Rights.