The crucial vote was returned in favour of banning the use of pesticides containing neonicotinoid chemicals that have been linked to a collapse of bee populations in scientific studies.
As a result, Europe will now enforce the world's first continent-wide ban on widely used insecticides that contain the chemical.
The European Commission had suggested that sprays containing the chemical should be restricted to crops not attractive to bees and other pollinators – however many farmers and crop experts argue that there is insufficient data, and that data from field studies is needed.
The Commission said that it wants the moratorium to begin no later than 1 July this year.
A report published by the European Food Safety Authority (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".
Some restrictions are already in place for neonicotinoids in France, Germany, Italy and Slovenia. However a previous motion for a two-year moratorium did not attract enough support last month, under the EU's weighted voting system, after the UK and Germany both abstained.
The new vote by the 27 member states of the European Union to suspend the potentially damaging compound was supported by most nations. but did not reach the required majority under EU voting rules.
Fifteen countries voted in favour of a ban - however this is not enough to form a qualified majority according to EU rules. The hung vote handed the final decision to the European commission (EC) who will now impose a two-year restriction on neonicotinoids.
"Since our proposal is based on a number of risks to bee health identified by the European Food Safety Authority, the Commission will go ahead with its text in the coming weeks," EU health commissioner Tonio Borg said after the vote.
"I pledge to do my utmost to ensure that our bees, which are so vital to our ecosystem and contribute over €22bn annually to European agriculture, are protected."
News of the ban was welcomed by environmental campaigning groups including The Soil Association and Friends of The Earth:
"This decision is a significant victory for common sense and our beleagured bee populations,” said Friends of the Earth's head of campaigns Andrew Pendleton. "Restricting the use of these pesticides could be an historic milestone on the road to recovery for these crucial pollinators."
Emma Hockridge, head of policy for the Soil Association commented that the vote result 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,” she said.