On February 20, the Supreme Court refused to consider the party's complaint in Russia's second largest city saying it was not within its jurisdiction. The Central Election Committee declared the decision lawful.
Sergei Popov, Yabloko deputy chairman, said the party was likely to appeal to the Constitutional Court.
In 2003, Yabloko won only four seats in Russia's 450-seat lower house of parliament. The party's poor performance was widely attributed to its failure to merge with another liberal bloc, the Union of Right Forces (SPS).
Since then, the State Duma has been increasingly dominated by the pro-Kremlin party United Russia.
Elections to local legislatures in 14 Russian regions will be held March 11. Seven regions have already completed registration of candidate parties.