Conceding defeat, Griffin said BNP supporters had voted for "Ukip's racist policies instead".
The BNP polled 32,826 in the north-west of England, equating to just 1.87% of the vote – down 6.13% on 2009, when Griffin and Andrew Brons, his former party colleague from Yorkshire, were elected to the European parliament.
This time around, the far right party also failed to hold Brons' Yorkshire seat, which he had decided not to contest after falling out with Griffin and leaving the party in 2012.
In the north-west, Labour increased their share of the vote by 13.86% to 33.86%, giving them three MEPs, up one on 2009. Lead candidate Theresa Griffin was heckled by her BNP namesake and his cronies after she used her victory speech to congratulate voters on rejecting the "hate driven policies of the BNP".
Ukip's deputy leader Paul Nuttall was re-elected, alongside first timers Louise Bours, a Brookside actor who used to go by the surname van de Bours, and barrister Steven Woolfe. Nuttall ended his victory speech by declaring "The age of four party politics has arrived."
The Tories lost one MEP in the north-west but kept two. The Greens trailed in fourth place, their vote slightly down on 2009, followed by the Liberal Democrats, whose MEP Chris Davies lost his job after the party's vote in the region dropped by 8.25%.
Responding to the evening's results, Tim Farron, the Liberal Democrats' despondent chair, said: "The only thing that will make me feel better walking out of here tonight will be knowing that Nick Griffin is no longer my MEP."
Arriving at Manchester town hall on Sunday night, Griffin came under attack from protesters shouting "Nazi scum off our streets". Some were rugby tackled by police after throwing placards at him reading "Nick Griffin Must Go", with one attempting to land a punch on the BNP man.
Speaking after his defeat, Griffin blamed Ukip for taking the BNP's vote. Asked whether the people of the north-west had rejected his party's racist and fascist policies, he said: "They've voted for Ukip's racist policies instead."
He added: "Ukip want to keep out white Poles but let in huge numbers of Pakistanis and Africans."
He said the BNP wasn't finished, pointing to its sole electoral success at the local elections last week, when Brian Parker was reelected for a third term in the Marsden ward of Nelson, Pendle. "That's the first seat we have won in three years. We are coming back," he said, adding that after years of debt problems, the BNP was "back in the black".
Griffin claimed he knew back in February he was going to lose his seat when campaigning in the byelection in the Greater Manchester constituency of Wythenshawe and Sale East, which was held by Labour.
"We put in a really good campaign in Wythenshawe and got a fantastic response from the public and it didn't translate into votes – that's when we knew," he said.
After six months on taxpayer-funded severance pay, he said he intended to campaign in the region - partly by setting up food banks exclusively for "our people".
He told Sky news that those who had switched allegiance from the BNP to Ukip would be disappointed: "I've lost count of the number I've spoken to who say, 'We really like the BNP but we are voting Ukip because there is more chance they will stop immigration and send them all home'," he said.
"As there is not a hope in hell of that, people are going to be very disappointed when they find out what Ukip really stands for and that huge vote is going to come back to us.
"Most of the voters are what the liberal elite call 'racist' - they want immigration stopped for good, the whole lot of them. They think they are going to get that with Ukip. They are not."
Griffin departed with a warning that the "people are waking up" as other anti-immigrant groups scored victories across the EU. He declared that the victory of the Front National in France was "good news" and drew a comparison with the rise of Ukip in Britain.
"While Front National is nearly as soft as Ukip, such votes show the people are waking up. Real change will follow," he said. Two men were arrested for breach of the peace after trying to punch Griffin as he arrived at the election count, Greater Manchester police said.
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