"TeliaSonera and Altimo disagree with the court's decision and believe that it is based on an insufficient analysis of facts and applicable rules and statutes," the Swedish-Finnish company said in a statement.
However, an appeals court rejected in October it on grounds that a foreign investor cannot take control of a Russian strategic company.
Litigation over the deal began after billionaire Alisher Usmanov, who owns a 39 percent stake in Megafon through TelecomInvest company, objected to the transaction in April.
TelecomInvest argued that the merger contradicts Russian law, which bans foreign companies from taking control of Russia's strategic companies.
TeliaSonera and Altimo hold respectively 43.8 percent and 25.1 percent stakes in Megafon, Russia's second largest operator, corresponding to a total 68.9 percent stake.
"Altimo and TeliaSonera believe that the agreement is fully valid and enforceable and does not contradict Russian or other applicable legislation or unlawfully infringe interests of any third party," Tuesday's statement said.
"Both companies disagree that a general agreement of intent can be challenged in court as contradictory to the Russian Foreign Investments Law," it added.