Participation slumped to an estimated 43 per cent, the lowest level since European elections began 30 years ago in 1979, as 213 million out of 375 million voters across the EU stayed at home.
"It does affect the legitimacy of the EU," admitted Margot Wallstrom, the European Commission vice-president.
Governments in Spain, Bulgaria, Hungary, Latvia, Greece and Ireland, all countries hit hard by the economic crisis, were punished by angry voters.
Support for centre-Left parties and governments crashed across the EU as fringe parties, not the Socialists, picked up protest votes while the centre-Right weathered the storm.
As polling stations closed on Sunday night, estimates put mainstream centre-Right parties to be the biggest group with control of up to 276 seats out of 736 in the European Parliament.
Anti-immigrant and far-right groups made significant gains in the Netherlands, Austria, Hungary, Denmark, Slovakia and Finland.
Geert Wilders and his far-Right anti-Islamic immigrant party shot to second place behind the ruling Christian Democrats by taking 17 per cent of the vote in the Netherlands.
In Austria too, two anti-immigrant far-Right parties took an unprecedented 17.7 per cent of the vote.
The far-Right Danish People's Party won two seats and took 14.4 per cent of Denmark's vote.
In Slovakia a low turnout of just 19.4 per cent propelled an anti-gipsy extremist ultra-nationalist into the parliament and Hungary's far-Right Jobbik took three seats for the first time.
Latvian voters protesting against high unemployment, looming currency devaluation and swinging public spending cuts punished their government by electing Alfred Rubiks, a former top communist official representing Latvia's Russian minority, as an MEP.
Mr Rubiks resisted Latvian independence from the Soviet Union in 1991 and later spent three years in jail for backing a coup to unseat the new government.
Spain's conservative opposition Popular Party took 42 per cent of the vote as economic discontent pushed the Socialists into second place with 38.6 per cent.
Greek voters, furious after a spate of corruption scandals and their government's handling economic crisis, handed the Socialists victory and a 10 point lead over the ruling conservative New Democracy party.
In Sweden, the Pirate Party, founded to legalise internet file sharing and to defend online privacy from state snoopers, took over seven per cent, taking a seat.
But centre-Right governments in Germany, France and Italy held their own.
In Germany, Angela Merkel's Democratic Union and its Bavarian sister, the Christian Social Union, won just over 38 per cent of the EU vote.
German Social Democrats were predicted to win only 21.3 per cent, their worst showing since the Second World War in a nationwide election.
In France, Nicolas Sarkozy's centre-Right UMP group was the big winner, with 28 per cent of the vote, as the opposition Socialists suffered serious losses, plunging the already weak party into further disarray.
According to exit polls, Silvio Berlusconi, Italy's prime minister, has consolidated his government despite his impending divorce and continuing revelations over his private life.
