The state-controlled Rosneft said in a statement it would purchase the assets for $629 million from Unitex, a firm that bought the facilities last month at auction.
Rosneft also owns what was Yukos's key production unit, Yuganskneftegaz.
Rosneft has been the main beneficiary of the Yukos bankruptcy sales, becoming Russia's biggest oil producer with production of over 2 million barrels per day.
Rosneft chief executive Sergei Bogdanchikov said earlier this week that the group was also in talks with a little-known company called Prana, which bought Yukos's Moscow headquarters offices last month.
Yukos, once Russia's biggest oil producer, was hit in 2004 with back-tax claims of billions of dollars.
The case was widely seen as a Kremlin attempt to quash Khodorkovsky's political ambitions.