The campaign in Sochi has been in the spotlight, with a host of high-profile candidates running. The city prepares to host the 2014 Winter Olympics and is set to receive billions of dollars in government funds.
Lebedev's spokesman Artyom Artyomov said the Sochi court excluded the billionaire for failing to provide a financial report required for registration, which he said could not be true as election officials would not have registered Lebedev without the required documentation.
He added that Lebedev would appeal the ruling, which he said proved the businessman was seen as the leading challenger to the Kremlin-backed candidate.
"The ruling will be appealed," Artyomov said. "The court ruling shows the authorities are treating him [Lebedev] as the main rival to [Anatoly] Pakhomov."
He also said formalities to remove Lebedev from the race could not be completed before the April 26 election.
Court officials have not commented on the ruling. Sochi election committee head Yury Rykov said he would adhere to the ruling when he received it.
Earlier on Monday, candidate Andrei Bogdanov said he was withdrawing from the race in favor of Pakhomov, the city's acting mayor, who was nominated by the ruling United Russia party.
Seven candidates are now running for Sochi mayor, including opposition politician Boris Nemtsov. Election authorities earlier denied registration to former Bolshoi Theater ballerina Anastasia Volochkova and human rights ombudsman Dmitry Berdnikov.
