Pakistan lost the seat in the Asia-Pacific category of the UN Human Rights Council in which five seats were vacant.
Pakistan failed to win a re-election to the top UN human rights body, managing to get just 105 votes in the 193-member General Assembly.
The General Assembly yesterday elected 18 members of the UN Human Rights Council through a secret ballot.
Pakistan's current term at the Council is set to expire on December 31 and it was seeking re-election to the 47-member Human Rights Council.
Sources said the loss came as a setback to the Pakistani delegation that had appeared confident of winning the seat. The loss has been attributed to the way the Pakistani delegation fought the election, and that it could not lobby effectively for the vote, said sources.
The new members, who will start their three-year terms beginning January 1 next year, are Belgium, Burundi, Cote d'Ivoire, Ecuador, Ethiopia, Georgia, Germany, Kenya, Panama, Kyrgyzstan, Mongolia, Philippines, Republic of Korea, Togo, Slovenia, Switzerland, United Arab Emirates and Venezuela.
Pakistan lost the seat in the Asia-Pacific category in which five seats were vacant.
India is also a member of the Council and its term will end in 2017.
Members of the Council are elected directly and individually by secret ballot by the majority of the members of the General Assembly.
Geneva-based non-governmental human rights group UN Watch welcomed the defeat of Pakistan, terming it as a "major surprise."
Days before the vote, several human rights bodies had opposed the re-election of Venezuela, Pakistan and UAE to the UN Human Rights Council due to widespread criticism of these governments for egregious human rights violations.
According to a report by UN Watch, Human Rights Foundations, and the Lantos Foundation, Pakistan, UAE, Burundi and Ecuador were cited by human rights groups for having committed serious violations of numerous articles of the Universal Declaration of Human Rights, including curbs on the freedoms of speech, press, religion, and assembly, along with disregard for fundamental due process.
The candidate countries were also found to have voted against UN resolutions taking action for victims of human rights abuses in various hotspots, UN watch said.
Sources in the Indian Mission to the UN here welcomed the election of Mongolia and Kyrgyzstan against the backdrop of historical visits undertaken by Prime Minister Narendra Modi to these nations earlier this year.