The ruling by the court in the Siberian city of Krasnoyarsk strips Vasily Shakhnovsky of his parliamentary immunity and leaves him open to prosecution for alleged tax-evasion that he has already been charged with.
An official said the court had upheld the prosecutor's view that correct procedures had not been observed in his election to the Federal Council.
The court ruling is the latest in a series of actions taken by prosecutors against Yukos, including the arrest of its chief Mikhail Khodorkovsky and the seizure of 42% of its shares.
Still in jail, Khodorkovsky has since resigned as the Yukos chief.
Another Yukos major shareholder Platon Lebedev is being held in jail on theft linked to a 1994 privatisation deal.
Parliament in Evenkiya voted for Shakhnovsky to become a senator a day after security police arrested Khodorkovsky on 25 October.
He has been spared pre-trial detention but is prohibited from leaving Moscow.