The final tally for the vote was 29 in favor, eight opposed and 16 abstentions. Russia, China and Bolivia were among the countries that rejected the measure.
The 22-year old woman died in police custody. The government contends Amini died of a heart attack while demonstrators claim she was beaten by the morality police, which arrested her for allegedly wearing a hijab improperly.
The US Mission to the United Nations authored the resolution and asked the members of the 54-member ECOSOC to vote in favor and remove "the ugly stain" from its credibility. Iran's mission to the UN urged the members to reject the draft.
Prior to the vote, Russia suggested asking for the legal opinion of the UN Legal Counsel. The majority of the countries, however, voted against considering the Russian proposal.
Later in the day, a spokesman for UN Secretary-General Antonio Guterres said that Guterres respects the decision of the member-driven body. The opinion was echoed by the president of the UN General Assembly, Csaba Korosi, who said he respects the "will" of the member states.
A UN source told Sputnik that Iran's removal from the body sets a bad precedent for the future.