Performing in black lingerie with the words "No Fear" scrawled on her back, Madonna attacked a city law adopted in March that imposed fines for spreading homosexual "propaganda". She had earlier called the law a "ridiculous atrocity".
The activists based their case on a video recording where they claimed Madonna could be seen trampling on an Orthodox cross and asking spectators to raise their hands with pink bracelets in support of the gay movement.
Judge Vitaly Barkovsky did not explain his decision but also ruled the activists should compensate legal expenses to companies which organized Madonna's concert. The activists said they will appeal the court ruling.
"Our position is the same. We believe there was a case of the breach of law, namely gay propaganda among minors," said activist Darya Dedova.
Homosexuality, punished with jail terms in the Soviet Union, was decriminalized in Russia in 1993, but much of the gay community remains underground as prejudice runs deep.