The ruling means that Khodorkovsky, once Russia's richest man, is set to be released in August 2014, and his partner Platon Lebedev would be set free in May 2014.
Their lawyers said they would appeal the ruling, which also upheld the 2010 guilty verdict. Khodorkovsky's father said he was disappointed by the "unlawful" verdict.
Khodorkovsky and Lebedev were arrested in 2003 and convicted in 2005 of evading taxes on the Yukos oil company in the case widely seen as President Vladimir Putin's revenge for Khodorkovsky's challenge to his power.
Last month, Europe's top human rights court dismissed claims that Khodorkovsky was prosecuted for political reasons in the first case, but said that some procedures during a trial against him were unfair.
Khodorkovsky's Yukos oil company was dismantled after his arrest, with its most lucrative assets ending up in the hands of state-owned Rosneft.
Khodorkovsky and Lebedev were convicted again in a second case in 2010 on charges of stealing oil from Yukos and laundering the proceeds. Last December, the Moscow City Court reduced their prison sentence from 13 years to 11 years.
Addressing the Supreme Court via video link from his prison colony in northwestern Russia, Khodorkovsky urged it to overturn what he called the "juridically illiterate verdict."
He said that the 2010 verdict, which found him guilty of stealing oil, was in contradiction to his first verdict, which found him guilty of not paying taxes on that same oil.
"We are not even talking here of the execution of the law, but of a willingness to destroy law as such, and the reputation of the judicial system, and trust in this state institution — merely for the sake of extending a prison term for opponents of the authorities," Khodorkovsky said.
Khodorkovsky's supporters fear that investigators are preparing yet another set of charges to keep him behind bars.
In May, Sergei Guriev, a leading liberal economist, fled Russia saying he wanted to escape pressure from a new probe focusing on an independent report that was critical of the 2010 verdict. Investigators claimed that its authors had a conflict of interest because they had previously received money from Khodorkovsky.
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