Nikolai Alekseev had filed suit against city authorities for what he described as an unfounded and illegal prohibition on holding the march in support of sexual minorities in Russia.
He said he would challenge the decision at the appeals court, and if necessary take his case to the European Court of Human Rights in Strasbourg.
Activists had planned to hold a gay pride march on central Moscow's Tverskaya Street, but were denied permission for a second year running by the city's conservative Mayor Yury Luzhkov, who has branded such events as "Satanic."
Around 100 protestors gathered nevertheless outside City Hall to submit a petition to the mayor requesting that he lift the ban.
The protest turned violent when a British gay rights activist was kicked and beaten by extremists, and police detained 31 people, including two Italians, in the ensuing melee.
A gay advocacy newspaper, Pink News, quoted the activist, Peter Tatchell, as saying: "The Moscow police gave right-wing extremists a more or less free hand to attack Gay Pride marchers. Despite many of us being battered left, right and centre, the police only arrested a handful of the assailants."
Demonstrators, who included European lawmakers, senior foreign human rights officials and celebrities, later gathered to submit a letter signed by around 50 members of the European Parliament protesting the ban and the violence.
Among those arrested were Marco Cappato, an Italian member of the EU parliament, and German MEP Volker Beck. The German politician told agencies that he and other protestors had been beaten by police, and denied that the gathering had been a demonstration, saying it was merely an attempt to submit a letter of protest.
Russia is a member of the Council of Europe, and a signatory to the European Convention of Human Rights, which obliges the state to allow demonstrations to be held.
Homosexuality was legalized in Russia in 2003, but discrimination against gays and lesbians remains widespread. The hostile crowd during the May demonstration included people carrying crosses and wearing Orthodox Church dress, along with ultra-nationalists.