The vote in the 15-member council was 12 in favor, with Lebanon abstaining and Brazil and Turkey voting against.
The vote was delayed for more than an hour after the ambassadors of Brazil, Turkey and Lebanon, three non-permanent members council members, said they had to await instructions from their governments.
The three countries finally decided to attend the meeting, but insisted on speaking before the vote to register their opposition.
The US-drafted resolution marked the fourth set of UN sanctions imposed on Iran since December 2006, as the international community has struggled in vain to curb the Islamic republic's nuclear ambitions.
Tehran maintains that its uranium enrichment program is for peaceful civilian purposes, while the Western nations have led accusations that it is seeking to develop an atomic weapon.
US Secretary of State Hillary Clinton on Tuesday called the sanctions "the most significant Iran has ever faced."
But the Brazilian UN envoy said the sanctions would increase the suffering of the Iranian people, and highlighted that Brazil and Turkey had brokered a nuclear fuel swap deal with Tehran which offered a pathway to a negotiated settlement.
Under the deal worked last month, Tehran agreed to ship 1,200 kilograms (2,640 pounds) of its low-enriched uranium to Turkey in return for high-enriched uranium fuel for a Tehran research reactor that would be supplied later by Russia and France.
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