The final results confirmed that Ukip, led by Nigel Farage, had the sixth Scottish seat in Brussels with a 10.4 per cent share of the vote.
The SNP won the election but failed in their aim of snatching a third seat, leaving Scotland represented by two MEPs from Alex Salmond's party, two from Labour, one Conservative and one Ukip.
Across Great Britain, Ukip emerged on top with 27.5 per cent of the vote, ahead of Labour who narrowly beat the Tories into third place.
Deputy Prime Minister Nick Clegg said he would not resign after the LibDem vote collapsed, costing his party all but one of its 12 MEPs elected five years ago.
Ukip, which seeks to limit immigration, doubled their share of the vote compared with the last European elections in 2009 to claim their first seat in any poll north of the Border.
Mr Farage, whose main campaign rally in Edinburgh was greeted by anti-racism protests, hailed the "breakthrough", while David Coburn, the party's new Scottish MEP, said: "The Ukip revolution has now come to Scotland."
But, as the recriminations began, Labour accused Mr Salmond of bolstering the party's support by turning the campaign into a straight fight between the SNP and what the First Minister repeatedly described as Mr Farage's "politics of intolerance".
Labour MEP David Martin said: "I'd like to suggest to David Coburn that the first thing he does when he sits down and recovers from the champagne is write a letter to Alex Salmond because there is no doubt in my mind that Alex Salmond's decision to polarise the campaign, the Scottish debate, between two extremes is why David Coburn is with us today as a member of the European Parliament."
In another provocative move Johann Lamont, the Scottish Labour leader, drew parallels between the SNP and Ukip.
She said: "From Poland to France, Greece to Scotland we have seen the rise of nationalism and Scotland now has three nationalist MEPs.
"Our task now is to change our politics from a politics of identity to a politics of ideas.
"Alex Salmond and Nigel Farage represent the same things, but our country deserves better than the simple analysis that our neighbours are the problem dressed up in saloon-bar charm."
The attacks followed Mr Salmond's complaint, made as results from around Scotland came in on Sunday night, that Mr Farage's party were boosted by "the wall-to-wall media coverage of Ukip that has been beamed into Scotland".
SNP MEP Alyn Smith hit back, saying: "Ukip topped the poll south of Border because the Westminster parties have pandered to their agenda.
"In Scotland, the SNP took them on - and we won the election."
He added: "The uncomfortable truth for Labour is that they are on the same side as Ukip, the most reactionary party in UK politics, in Scotland's independence referendum."
Speaking after the results were declared in Edinburgh, Deputy First Minister Nicola Sturgeon said there was "a world of difference" between Ukip's fourth place in Scotland and topping the poll across Britain.
She warned: "There can now be no doubt that the only threat to Scotland's place in Europe - and our ability to bring jobs and investment to Scotland - is the Ukip agenda that is dictating the terms of Westminster politics.
"That agenda is the exact opposite of what Scotland needs, which is why we need to build our own relationship with our European neighbours as an independent country - something that only a Yes vote in September can secure."
The SNP won the election with a 28.9 per cent share of the vote, down slightly on the party's performance in 1999, after the final votes from the Western Isles, where counting took place yesterday, were included.
Under the proportional voting system, the Nationalists would have required one-third of the vote to take Scotland's sixth seat and hold off the Ukip challenge.
Labour finished second with 25.9 per cent, up five points, ahead of the Conservatives on 17.2 per cent, whose new MEP Ian Duncan replaces Struan Stevenson, who stood down.
The LibDems' share of the vote plummeted to 7.1 per cent as they lost their only MEP in Scotland while being beaten to sixth place behind the Greens on eight per cent.
Turnout in Scotland was 33.5 per cent, five points higher than in 2009.