The ruling is highly unusual in a country where critics say courts usually shield the government from responsibility and many doubt that the high-profile officials handling the controversial rescue operation will ever be prosecuted.
Moscow's Lefortovsky district court said the refusal of the powerful Investigative Committee to launch a criminal probe into the handling of the rescue operation was "illegal and unjustified," court spokeswoman Yulia Skotnikova told AFP.
The decision came in response to a complaint from Igor Trunov, a high-profile lawyer representing victims' relatives and survivors of the theatre hostage crisis who seek justice from the authorities.
"We have had to wait for this for a decade," Trunov told AFP. "The court decision came as a surprise, of course."
A total of 912 people, many of them children, were held hostage in Moscow's Dubrovka theatre by Chechen militants for three days in October 2002. The audience had been watching a light musical called "Nord Ost".
The crisis ended on October 26 when special forces filled the building with an unknown gas to neutralise the attackers, who had threatened to blow up the venue unless Russia pulled its troops out of Chechnya.
A decade after the tragedy, survivors and victims' relatives remain highly critical of how the authorities handled the crisis.
Following the rescue operation, Boris Nemtsov, an opposition figure who was a lawmaker at the time, called for an investigation into possible negligence by officials but authorities refused to open a criminal probe in 2002.
Last year, the European Court of Human Rights ordered Russia to reopen its investigation into the victims' deaths and possible negligence by officials, but the Investigative Committee, the Russian equivalent of the US FBI, refused to do so.
The Investigative Committee has 10 days to appeal the ruling.
Critics charge that Russia's high-ranking security officials should have been punished for letting the Chechen militants seize a Moscow theatre in the first place as well as sanctioning the use of the deadly gas.
Instead, several of them including Vladimir Pronichev, former deputy head of FSB security service who was in charge of the crisis task force at the time, have received the Hero of Russia awards, the country's top honour.
Sergei Kovalyov, one of best-known Soviet-era dissidents who has been highly critical of President Vladimir Putin, said the top security officials handling the hostage crisis should be taken to court.
"Who gave the green light for this (gas) method?" Kovalyov told the opposition newspaper Novaya Gazeta.
"You do not have to read tea leaves. Maybe he (Putin) was not the author of the plan but he of course sanctioned this action."
Trunov, the victims' lawyer, said rather than Putin himself it was the medics, firefighters and former Moscow mayor Yury Luzhkov who should be held responsible for the "whole spectre of egregious crimes" that took place.
"Instead of taking unconscious people (out of the theatre), they stripped them of their furcoats," he claimed.
"Plundering (at sites of tragedies) is a widespread phenomenon in Russia. They undress corpses everywhere but in Russia no-one fights it."
Many victims say their health has been affected but many cannot receive proper treatment because to this day they do not know what kind of gas has been used on them.