Garry Kasparov, former world chess champion and leader of the Other Russia party, and Roman Dobrokhotov, the leader of We, a youth opposition movement, were also arrested during separate protests in the capital.
Also on Saturday, about 1,000 Communist demonstrators rallied on a central square in Moscow, surrounded by heavy police cordons.
Addressing the crowd, Gennady Zyuganov, the Communist party chief, urged the government to abandon Western economic models and undertake broad nationalisation policies.
Several hundred police blocked the square, but did not try to break up the protest, which had been sanctioned by the authorities.
In the far eastern port of Vladivostok, about 2,500 people marched to denounce a planned increase in car import tariffs, and some also shouted slogans urging Putin to resign.
The protests reflect growing public anger over economic conditions in Russia and pose a challenge to the Kremlin, which has benefited from years of an oil-driven boom and a fragmented opposition.
But despite the protests, support for Putin is not substantially waning in Russia.
A poll conducted last week by the Levada Institute of Moscow showed that 83 per cent of the public approve of Putin's work as prime minister.
Saturday also saw pro-government demonstrations with organisers saying that at least 5,000 people had gathered outside the Kremlin, shouting slogans in favour of Putin and Dmitry Medvedev, the Russian president.
Police put the number at 8,000 people.
Opposition groups, which lack parliamentary representation, hope to benefit from the increasing severity of the economic crisis in Russia, which has so far cost thousands of jobs and seen delays in wage payments.
The Russian rouble has also seen a rapid devaluation over the last six months, while the federal budget is predicted to be in deficit this year for the first time in a decade.