The committee dismissed the party's complaint against the decision, saying that of the 20% of the signatures examined, 11.97% had been falsified.
However, Yabloko insisted that only 10.43% turned out to be invalid, representing a shortfall of only 0.43% of the number needed to be registered, according to Russian electoral law.
"The decision of St. Petersburg Election Committee was made within the framework of the law," the commission said.
In January, the Election Committee in the North Caucasus republic of Dagestan also refused to register Yabloko for regional legislative elections in March, saying that more than 10% of the signatures in support of the party had been doctored.
Yabloko leaders said the refusal was a political move designed to neutralize the opposition.
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 the registration of candidate parties.
