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 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.
Khodorkovsky's Yukos oil company was dismantled after his arrest, with its most lucrative assets ending up in the hands of state-owned Rosneft.
The two 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."
Khodorkovsky said the 2010 verdict was a "flagrant display of scorn for the law" driven by "irrational fears of government officials" at seeing him and Lebedev free.
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