Over 600 fans of the Moscow club had gathered at the prosecutors' office late Tuesday to demand a probe into the death of a Spartak supporter shot in a clash with migrants from Russia's North Caucasus, daily newspaper Kommersant said.
Videos posted on the popular blogging hub LiveJournal showed fans standing on cars, lighting green and red flares and halting traffic on Moscow's Leningradsky Prospekt.
Crowds chanted the nationalist slogan "Russia for Russians!" before they were dispersed by riot police.
Russia's chief investigators office said it would take charge of the probe into the death in the wake of the protests.
"The decision was made taking into account the wide social response sparked by this crime," Investigative Committee spokesman Vladimir Markin was quoted by the Interfax news agency as saying.
Russia's active football fan clubs have raised concern among human rights activist, who view them as a fertile ground for a violent new brand of Slavic nationalism they say may cause racist violence.
Last month, at least 1,000 Zenit St Petersburg supporters - who have a fearful reputation for violence in Russia - clashed with riot police and smashed bus stops in Russia's second largest city after their team won the domestic league.
