Participants held up candles and pictures of the journalist and spoke in remembrance of Politkovskaya, a sharp critic of Kremlin policies in Chechnya, who was shot inside her Moscow apartment building in 2006.
The meeting, attended by numerous opposition figures, was unusual in that had received prior official approval from city authorities.
The low-key anniversary ceremony took place against the backdrop of nationwide celebrations to mark the 60th birthday of President Vladimir Putin, which falls on the same day.
The U.S. State Department said Saturday it would "continue to shine the spotlight on (Politkovskaya's) case" and urged more protection for journalists worldwide that speak out against abuses.
Rights organization RAW in WAR, which annually recognizes achievements by women reporting in conflict zones, demanded Russia bring to justice the killers of Politkovskaya and Natalia Estemirova, a rights activist in Chechnya murdered in 2009.
"We call again on the Russian government ... to end the killings and persecution of journalists and human rights defenders in the Russian Federation," read the group's statement, which was signed by a committee including dozens of international activists and public figures.