The US captured Abu Zubaydah and Abd al-Rahim al-Nashiri after the September 2001 attacks in the US and they are now at the Guantanamo Bay prison.
The CIA operated secret prisons, including in Lithuania and Romania.
The European Court of Human Rights (ECHR) said both countries had assisted US ill-treatment of the two suspects.
The existence of the so-called CIA "black sites" for interrogation - under so-called "secret rendition" - was kept secret for many years after 9/11.
Abu Zubaydah, a stateless Palestinian born in Saudi Arabia, is thought to have been al-Qaeda's chief recruiter in the 1990s, and later became a key organiser, linking Osama Bin Laden to other al-Qaeda cells.
Saudi-born Abd al-Nashiri led al-Qaeda's operations in the Gulf region, according to US intelligence.
