There is great concern across Europe about the collapse of bee populations.
Neonicotinoid chemicals in pesticides are believed to harm bees and the European Commission says they should be restricted to crops not attractive to bees and other pollinators.
But many farmers and crop experts argue that there is insufficient data.
Fifteen countries voted in favour of a ban - not enough to form a qualified majority. According to EU rules the Commission will now impose a two-year restriction on neonicotinoids - and the UK cannot opt out.
The Commission says it wants the moratorium to begin no later than 1 July this year.
The UK did not support a ban - it argues that the science behind the proposal is inconclusive. It was among eight countries that voted against, while four abstained.
Wild species such as honey bees are said by researchers to be responsible for pollinating around one-third of the world's crop production.
There is heated debate about what has triggered the widespread decline in bee populations. Besides chemicals, many experts point to the parasitic varroa mite, viruses that attack bees and neglect of hives.
After Monday's vote the EU Health Commissioner, Tonio Borg, said "the Commission will go ahead with its text in the coming weeks".
"I pledge to do my utmost to ensure that our bees, which are so vital to our ecosystem and contribute over 22bn euros (£18.5bn; $29bn) annually to European agriculture, are protected."
Greenpeace EU agriculture policy director Marco Contiero said Monday's vote "makes it crystal clear that there is overwhelming scientific, political and public support for a ban.
"Those countries opposing a ban have failed."
An EU vote last month was inconclusive, so the Commission proposal went to an appeals committee on Monday - and again the countries were split on the issue.
Some restrictions are already in place for neonicotinoids in France, Germany, Italy and Slovenia.
The three neonicotinoids are clothianidin, imidacloprid and thiametoxam.
A report published by the European Food Safety Agency (EFSA) in January concluded that the pesticides posed a "high acute risk" to pollinators, including honeybees.
However, it added that in some cases it was "unable to finalise the assessments due to shortcomings in the available data".Intensive lobbying
There was ferocious lobbying both for and against in the run-up to Monday's vote, the BBC's Chris Morris reports from Brussels.
Nearly three million signatures were collected in support of a ban. Protesters against neonicotinoids rallied in Westminster on Friday.
Campaign organiser Andrew Pendleton of the environmental group Friends of the Earth said "leading retailers have already taken action by removing these pesticides from their shelves and supply chains - the UK government must act too".
Chemical companies and pesticide manufacturers have been lobbying just as hard - they argue that the science is inconclusive, and that a ban would harm food production.
The UK government seems to agree with the industry lobby. It objected to the proposed ban in its current form. The chief scientific adviser, Sir Mark Walport, has said restrictions on the use of pesticides should not be introduced lightly, and the idea of a ban should be dropped.
The EU moratorium will not apply to crops non-attractive to bees, or to winter cereals.
It will prohibit the sale and use of seeds treated with neonicotinoid pesticides.
And there will be a ban on the sale of neonicotinoids to amateur growers.
There have been a number of studies showing that the chemicals, made by Bayer and Syngenta, do have negative impacts on bees.
One study suggested that neonicotinoids affected the abilities of hives to produce queen bees. More recent research indicated that the pesticides damaged their brains.
But the UK Department for Environment, Food and Rural Affairs (Defra) argues that these studies were mainly conducted in the laboratory and do not accurately reflect field conditions.
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