The vote was 22-1, with 12 abstentions on the 35-nation board of the International Atomic Energy Agency, IAEA spokeswoman Melissa Fleming told reporters.
The resolution finds Iran in violation of international nuclear safeguards, but referral to the Security Council, which could impose sanctions, would only come after a report on Iran by IAEA chief Mohammed ElBaradei, which he will probably make to the next board meeting in November.
The meeting started over two hours late with Russia trying to get the EU to agree to amendments that would have eliminated the automatic requirement of referral to the Security Council.
But the amendments were not accepted, and the resolution was approved in the same form as proposed Friday by Britain. The only vote against was Venezuela while Russia, which had expressed bitter opposition to the resolution, abstained. India, a member of the non-aligned movement that had opposed the resolution, voted for it.
Russia has an $800-million contract to build Iran's first nuclear reactor, China, buys Iranian oil where as non-aligned states fear that referral would escalate the Iranian nuclear crisis.
EU negotiators Britain, France and Germany, as well as the United States, were confident they have enough votes to have the resolution adopted, if consensus can not be achieved.
British, French and German foreign ministers consulted Friday ahead of the board meeting as the crisis deepened.
"The EU-3 held firm," a Western diplomat said.
Iran ready to hit back
Iran meanwhile was expected to react strongly if the resolution were adopted, diplomats said, threatening to make nuclear fuel in a move that could lead the West to advance the calendar for getting the Security Council involved.
Iran has said it will submit a note in writing to the IAEA saying that it will begin to enrich uranium, the nuclear reactor fuel that can also be bomb material, and also cease applying a protocol for wider IAEA inspections if the resolution is adopted, a diplomat close to the IAEA said.
Another diplomat said Iranian representatives had already at Friday's meeting showed ElBaradei two unsigned letters as a "threat" that they could be signed and filed to signal Iran's going ahead with uranium enrichment and reducing cooperation with IAEA inspections.
Iran has a 164-cascade of centrifuges for enriching uranium at a facility in Natanz in the center of the country but has held off from activating it as a confidence-building measure for talks on its nuclear program.
The draft resolution was the weaker of two texts the EU had prepared in an effort at compromise to garner support on the IAEA board, as it delays immediate referral of Iran to the Security Council.
Western diplomats said it would be unfortunate not to have the united message that consensus represents, but that a vote is still better than not taking action to force Iran to guarantee it is not developing nuclear weapons.
Softer measures if Iran cooperates
Non-aligned nations, which make up 14 of the 35-nation board, has earlier threatened to boycott Saturday's session, which would deny the two-thirds quorum needed for a vote, but it was not clear it they would hold to this.
Citing Iran for non-compliance, which requires the IAEA to at some point bring the Islamic Republic before the Security Council, would be a major development almost three years into an IAEA investigation that has documented two decades of hidden Iranian nuclear activities.
Iran's resumption last month of uranium conversion, a first step in making enriched uranium, set off a crisis in which the United States and the EU want to call in the international weight of the Security Council, which could impose trade sanctions although softer measures are at first expected.
Iran's re-suspending conversion could lead to referral being put off even longer. And if Tehran showed full cooperation with the IAEA, it could end up being reported for this in an "information" report that would not threaten sanctions, diplomats said.
The IAEA had on August 11 called on Iran to cease conversion but hardline Iranian President Mahmoud Ahmadinejad (photo) proclaimed in a speech to the UN General Assembly in September Tehran's "inalienable right" to nuclear fuel work, an uncompromising stance that angered
The draft resolution says that an IAEA investigation since February 2003 has uncovered a "history of concealment of Iran's nuclear activities" which has led to a lack of confidence "that Iran's nuclear program is exclusively for peaceful purposes" and to "questions that are within the competence of the Security Council as the organ bearing the main responsibility for the maintenance of international peace and security."