Nearby, a rally of several thousand was held close to the Kremlin in support of Russian intervention in Crimea.
Crimea's referendum Sunday has been loudly condemned as illegitimate by much of the international community. As heavily armed forces apparently under Russian command have effectively taken control of the peninsula, the vote to join Russia has been widely criticized as a mere formality.
Russian support for reclaiming Crimea majority has intensified amid weeks of relentless state television coverage of purported aggression toward ethnic Russians by the new Kiev government, which came to power after Ukraine's Moscow-friendly president, Viktor Yanukovych, fled the country in February.
While President Vladimir Putin's ratings have risen since he announced Russia's willingness to use force in Ukraine, the anti-government demonstration Saturday showed that not everyone is happy with the decision.
"I love Ukraine — it's Putin who needs war and an empire, not me," said Dmitry Maksimov, a 29-year-old lawyer who held a bouquet of flowers dyed blue and yellow, the colors of the Ukrainian flag.
Nadezhda Tolokonnikova, a member of Pussy Riot, called for defiance against the authorities.
"Don't believe it when they say that we are few, that we are weak. Together we will change this country," she said in a speech from a stage.
None of Russia's state-owned news channels showed footage from the anti-government protest, and instead showed live video from the rally near the Kremlin, where large gangs of men from a group called "Essence of Time" dressed in uniform red jackets and marched to the sound of Soviet-era military music in disciplined columns.