But the European Court of Human Rights found that their trial had been unfair and that their 2005 sentencing to a remote jail near the Arctic Circle was unjustified.
Khodorkovsky, a staunch critic of President Vladimir Putin and once Russia's richest man, was arrested in 2003 and handed alongside Lebedev 13 years jail on charges of multi-million dollar tax evasion and money laundering.
"Charges against two Russian business executives had a sound basis, but the hearing of their case was unfair, and their placement in remote penal colonies unjustified," the Strasbourg-based court said.
Judges from the court ordered Moscow to pay 10,000 euros ($13,200) to Khodorkovsky in damages.
The punishment, which in December was reduced by two years allowing the two men to walk free in October 2014, was seen by supporters as a politically-motivated act of revenge.
Thirteen people have been freed so far as part of an amnesty for Russia's jailed entrepreneurs intended to correct failures in Russia's legal system, which has often seen entrepreneurs jailed on trumped-up charges.
However it applies only to those who have been convicted once and agree to repay damages - ruling out Khodorkovsky, who was convicted of fraud again in 2010.
Khodorkovsky, now 50, was one of the young tycoons who built fortunes after the Soviet Union's 1991 collapse.
Both sides have three months to appeal the court's decision.
(Reporting By Gilbert Reilhac; writing by John Irish; editing by Mark John)