Clothianidin, thiametoxam and imidacloprid have been banned after an EU vote.
The European Commission will now restrict the use of the neonicotinoids 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.
The Commission says it wants the moratorium to begin no later than 1 July this year.
The UK was among eight countries that voted against a ban, while four abstained.
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 22 billion euros annually to European agriculture, are protected."
Friends of the Earth head of campaigns Andrew Pendleton said: "This decision is a significant victory for common sense and our beleagured bee populations.
"Restricting the use of these pesticides could be an historic milestone on the road to recovery for these crucial pollinators.
"But pesticides are just one of the threats bees face - if David Cameron is genuinely concerned about declining bee numbers he must urgently introduce a Bee Action Plan.
"The UK Government's refusal to back restrictions on these chemicals, despite growing scientific concern about their impact, is yet another blow to its environmental credibility.
"Ministers must now help farmers to grow and protect crops, but without relying so heavily on chemicals – especially those linked to bee decline."
The Soil Association welcomed today’s decision. Emma Hockridge, Soil Association head of policy said:
"This is a victory not only for the bees and other pollinators, but for independent science against the political, pro-pesticide position adopted by UK Environment Secretary Owen Paterson and the pesticide industry. The European Commission and many European governments have reacted responsibly to the British and European scientific evidence showing clearly that a suspension is justified."