Wreaths were also laid by Estonian WWII veteran organizations.
The Soviet-era World War II monument was removed from central Tallinn to a military cemetery two weeks ago.
The monument's relocation sparked a wave of protests, both in Moscow and Tallinn.
Protests in Tallinn, mostly by ethnic Russians, left one Russian dead and hundreds under arrest. Moscow said the protests were "a natural reaction" and accused Estonian police of human rights violations.
Estonia, an EU and NATO member since 2004, said it had been forced to close its consulate and evacuate diplomats' families from the capital accusing Moscow of dragging its feet in curbing the unrest and, even of, orchestrating it.
The EU and NATO formally backed Estonia. They demanded Moscow comply with the Vienna Convention and said the Baltic state was within its rights to move the monument, known as the Bronze Soldier.
The Bronze Soldier and other Soviet-era monuments have been a source of diplomatic tensions between Moscow and Tallinn for years. They have also provoked clashes between the Russian-speaking minority and Estonian radicals, who view them as symbols of Soviet occupation that began in 1940 and ended when the Baltic state regained its independence in 1991.
Relations between Russia and Estonia hit their lowest after Estonian authorities dismantled the monument ahead of Victory Day, which is marked May 9 in Russia, saying it was a reminder of 50 years of Soviet occupation. The monument is dear to Russians as a symbol of victory over the Nazis.
President Vladimir Putin congratulated the people of Russia earlier Wednesday on the 62nd anniversary of victory against Nazi Germany in a speech at a military parade in Moscow.
"We bow our heads to the courage and fortitude of all those who crushed the aggressor and stopped Nazism," he said.
He said Victory Day is the dearest holiday not only for the Russian citizens but also for the people of the former Soviet Union, the countries of Europe and the entire planet.
Putin cautioned against any attempts to obliterate the memory of those who died in the Great Patriotic War and desecrate monuments to war heroes.
Russian Foreign Minister Sergei Lavrov on Monday accused the European Union and NATO of conniving with countries that disrespect the memory of Soviet soldiers and seek to rewrite history.