The majority decision to refer Syria to the UN Security Council in New York reflects deep divisions within the IAEA's board of governors.
The 14 countries - mainly European and North American - who had co-sponsored the resolution were joined by only three more of the 35-strong board.
Six countries voted against, including China and Russia; 11 abstained and one was absent - so it was hardly a resounding condemnation.
Israel's air strike - on what the IAEA now accepts was a Syrian nuclear reactor still under construction near Deir Alzour in the country's remote north-east - took place in 2007.
The matter was referred to the IAEA the following year.
Syria consistently refused to answer the agency's questions or to provide the level of access to this - and other sites - that its inspectors required.
So why has it taken until now to cone to a vote at the IAEA board?
Washington has long been eager to refer Syria to the UN.
But many of its European allies were more cautious, still eager to see if Syria's young president could be won over and weaned from his alliance with Iran.
In any case the IAEA's board remained deeply divided. Many developing countries were suspicious of Washington's intentions. And western powers had their hands full persuading Moscow and Beijing to back tougher measures against Iran.
So what has changed to bring the Syrian issue to a vote? When the new IAEA Director General Yukiya Amano was elected to office he was determined to resolve the Syrian issue one way or another.
But he had won office after a divided vote where, as nuclear expert Mark Hibbs told me, the Syrian issue risked becoming "a flashpoint".
So, he explained, Mr Amano set out on "a cautious but deliberate twin-track strategy".
One track, when he was appointed director general at the end of 2009, was to avoid a rush to judgement, to keep asking questions.
He wanted to work with the Syrians and to give them sufficient time to co-operate with the agency.
However, at the same time, he sought to get more intelligence information from member states.
The US, says Mr Hibbs, eventually provided a large body of material to underpin the US/Israeli allegations - a lot of it highly sensitive intelligence.
Mindful of past problems between the agency and Washington - they disagreed fundamentally over their assessment of Iraq's nuclear programme in 2003 - Mr Amano sought as far as possible to verify this material from the IAEA's own sources.
Mr Amano was desperate to avoid polarising the IAEA board further. But his eventual conclusion inevitably prompted the board to line up on familiar lines.
For the US and many of its allies this has been a largely technical matter - Syria has broken the rules and needs to be held to account. This was, according to US Ambassador to the IAEA Glyn Davies, "one of the most serious safeguards violations possible".
The Russians were not so much countering that case but arguing, instead, that a referral to the Security Council was not necessary.
"The site at Deir Alzour no longer exists and therefore poses no threat to international peace and security," said a Russian statement.
But, of course, there is a huge dose of politics in this as well.
Mr Hibbs notes that over the past three years - and especially since the Syrian government's clamp-down on demonstrations, the attitude to Damascus - especially in Europe, has changed significantly.
"It is not a coincidence that the resolution that passed today did so when there is a very different atmosphere in the West towards the Syrian regime," he said on the phone from Vienna.
So the matter now goes to the Security Council in New York.
But, according to Mr Hibbs, the world should not hold its breath for UN sanctions against Syria.
With two of the five permanent Security Council members voting against the IAEA resolution, any sanctions attempt would be voted down.
Of course, there is already another battle over Syria being waged at the UN with several western countries pushing for a resolution condemning President Bashar Assad's repression against his own people.
Here too the views of Moscow and Beijing may prove decisive.