The court in the northwestern town of Velsk, near where Lebedev is serving time, ordered that his sentence be reduced by three years and four months. Judge Viktor Ivanov said the decision was based on a change in Russian laws, the RIA Novosti news agency reported.
It was not yet clear whether Khodorkovsky's sentence would be shortened as well. He would need to appeal to a separate court near where he is imprisoned in Karelia, also in northwestern Russia.
Both men were arrested in 2003 in a case widely seen as politically motivated after Khodorkovsky, then Russia's richest man, challenged the power of Vladimir Putin early in his presidency.
Khodorkovsky and Lebedev were convicted in 2005 of evading taxes on the Yukos oil company. They were tried together again in a second case and convicted in 2010 of stealing oil from Yukos and laundering the proceeds.
Lebedev has been in jail since July 2003 and is now set to be released in March 2013.
"It seems to me that this is one of the good signs that society has long awaited," said Mikhail Fedotov, who heads a presidential advisory council on human rights and civil society, RIA Novosti reported.
Wednesday's decision came as a Moscow court prepares to issue a verdict in the controversial case of three feminist punk rockers who were arrested after an anti-Putin protest in Moscow's main cathedral. Prosecutors have asked the court to send them to prison for three years.