Protesters chanted slogans against the ruling party as the Putin loyalists beat drums and chanted "Putin, Russia". Riot police arrested a number of protesters, including veteran liberal politician Boris Nemtsov.
Monday saw Moscow's biggest protest in years against alleged election fraud at Sunday's parliamentary election. Mr Putin has played down losses by his party, United Russia, which won but with just under 50% of the vote, a sharp drop in its support.
Correspondents say the result reflects Mr Putin's declining popularity ahead of his bid for the Russian presidency in March. Observers from the Organisation for Security and Co-operation in Europe (OSCE) say the election was slanted in favour of Mr Putin's party, United Russia.
The jerky footage, broadcast over the internet by the Russian citizen journalism outlet Ridus (audio in Russian), also appeared to show police intervening.
Correspondents say Mr Nemtsov and other protesters were hauled off to waiting police vehicles.
On Monday, police made at least 300 arrests and two key figures in the protest were both jailed for 15 days on Tuesday.
Well-known anti-corruption blogger Alexei Navalny was convicted of obstructing the course of justice and Ilya Yashin, leader of the Solidarity party, was convicted of a similar offence.
The arrest of the two men was heavily tweeted by Russian bloggers, who circulated photos of Mr Navalny and others in custody.
"There is not a single doubt that my case is under the special control of the party of crooks and thieves," he told reporters in court ahead of being charged, referring to United Russia. The Russian interior ministry has denied any extra security measures in Moscow, saying that police and troop movements in the city were a "rotation".
Its press service told Interfax news agency that 51,500 police including 2,000 interior troops had been on a state of alert since 1 December, as part of election preparations.
"Statements that extra forces are being drafted into Moscow do not correspond to reality," it said.