The insecticides – imidacloprid and clothianidin produced by German Bayer, and thiamethoxam, made by Switzerland's Syngenta – are used to treat seeds, and are applied to soil or sprayed on bee-attractive plants and cereals.
However, they have been blamed for a sharp decline in global bee populations.
The EU’s health commissioner, Tonio Borg, says the move protects the 22 billion euro European agricultural industry.
Bees account for 80 percent of plant pollination by insects, vital to global food production. Without them, many crops would be unable to bear fruit or would have to be pollinated by hand.
Fifteen nations voted for the ban, with eight against and four abstentions.
Although a majority of nations voted to save Europe's bees, under the EU's complex voting system that takes the population into account, the vote was 187 for, 125 against and 33 abstentions, short of a qualified majority but leaving the ultimate decision in the hands of the European Commission.
The European Commision said the ban will come into force in December.
Countries opposed to the ban, including Britain and Hungary, failed to muster enough support to block the Commission's proposed moratorium despite intense lobbying from pharmaceutical groups and farmers.
"Today's vote makes it crystal clear that there is overwhelming scientific, political and public support for a ban," said Greenpeace's Marco Contiero.
Germany, which in a previous vote had abstained and was under heavy pressure from pharmaceutical firms and farmers to fight the proposal, also voted in favour.
In February, a study published in the Journal of Science showed that falling numbers of wild bees and other pollinating insects are hurting global agriculture.
Pesticide producers Bayer of Germany and Switzerland's Sygenta, the top player on the global agrichemical market, have rejected claims that their products are at fault in the fall of bee numbers and say studies behind the suggested ban are based on flawed science.
Internet-based global campaigner Avaaz, which has gathered 2.5 million signatures to save the insect, floated a giant plastic honey bee over EU headquarters to hammer home its message.
Copa Cogeca, which represents European farmers and European agri-cooperatives, last week said even a temporary ban would cause 2.8 billion euros of losses to farmers and a further 2.0 billion to the EU economy due to a fall in seed production and rising feed costs due to a need to increase imports.