Hungary and Croatia will represent Eastern Europe on the council instead of Russia. Rights groups had called out Russia and Saudi Arabia, which was elected, for attacks on civilians in Syria and Yemen.
On Friday, Russia failed to secure re-election to the UN Human Rights Council (UNHRC), capping a campaign by the rights group to dismiss Moscow over its role in the conflict in Syria.
The 193-member UN General Assembly elected Croatia and Hungary to represent Eastern Europe on the rights council instead.
Hungary received 144 votes, while Croatia only narrowly edged ahead of Russia, collecting 114 votes to Russia's 112.
It is the first time since 2006 that Russia will not be a member of the Geneva-based council.
The 47 spots on the UNHRC are distributed on a regional basis in a staggered election process. The Council sees a third of its members re-elected every year. Members are tasked with monitoring and investigating rights violations worldwide.
Friday's newly elected countries begin their three-year term in January.
Rights groups question Russia and Saudi Arabia's record
Up to 80 human rights groups and NGOs, including Human Rights Watch and Refugees International, signed a petition urging countries to "question seriously whether Russia's role in Syria, which includes supporting and undertaking military actions which have routinely targeted civilians and civilian objects, renders it fit to serve on the UN's premiere intergovernmental human rights institution."
Rights groups and many governments accuse Moscow of conducting an indiscriminate bombing campaign on besieged rebel-held areas in the Syrian city of Aleppo. Around 250,000 civilians in the east of the city are living under siege with food rations expected to run out soon, according to the UN.
Russia dismissed the petition as "cynical" and "dishonorable." It claims its military operations in Syria are legal.
Rights groups also called out Saudi Arabia for its attacks against civilians in Yemen. They warned that the election of Saudi Arabia to the Council risked weakening the UNHRC's capacity to hold abusers to account. However, it was re-elected with 152 votes.
Other controversial members include China, which has been widely criticized for rights abuses, as well as Cuba and Egypt, both of which have dubious domestic rights records.
Other elected members also include Brazil, Britain, Iraq, Japan, South Africa and the United States.
dm/sms (AFP, Reuters)