Pavel Markov, the arbitration court judge, pronounced the ruling on Tuesday.
The ruling marked the end of a three-year back tax campaign which many considered an attempt by the state to regain control of the strategically important oil sector.
The fraud investigation against Mikhail Khodorkovsky, Yukos' billionaire founder, and the tax probe into the company that began in 2003 were cast by the Kremlin as a just crusade against a rotten corporate empire.
But many think it was punishment for Khodorkovsky's perceived political ambitions.
He was convicted last summer and jailed for nine years.
Analysts expect that state-controlled gas monopoly OAO Gazprom and state-controlled oil company OAO Rosneft, which became the third biggest oil producer overnight after acquiring Yuganskneftegaz from Yukos in a disputed auction in 2004, will acquire remaining assets in the course of the liquidation.
Both companies are being primed as national champion energy companies capable of competing with the likes of Exxon Mobil Corp. and Saudi Arabia's Aramco.
Gazprom has expressed an interest in the Yukos Tomskneft production unit, while Rosneft has said it will consider all potential purchases that appear on the market.
Rosneft is already Yukos' biggest creditor after the federal tax service, and could see its position strengthened by a further US$8billion in claims admitted by a court on August 10.