Diane Dodds has spoken of her party's disappointment in their result, blaming a split in the unionist vote
The DUP has had its worst ever European election result.
The party had previously topped the poll in every European election since 1979.
However, on Monday, its candidate Diane Dodds took the third of Northern Ireland's three MEP seats at the third stage without reaching the quota.
The DUP had 32% of the entire first preference vote in 2004, this time it has fallen to 18.2%.
"We are obviously very disappointed that because of the split in unionism - something we warned about - that Sinn Fein has topped the poll," said Diane Dodds.
Former DUP MEP Jim Allister, now the leader of Traditional Unionist Voice, polled more than 66,000 votes, but was later eliminated.
Sinn Fein's Bairbre de Brun has topped the poll. Ms de Brun got 126,184 votes and was the only candidate to reach the quota on the first count.
Jim Nicholson of the Ulster Conservatives and Unionists was the second MEP returned, elected at the third stage.
FIRST PREFERENCE VOTES
Agnew, Green Party - 15,764
Allister, Traditional Unionist Voice - 66,197
De Brun, Sinn Fein - 126,184
Dodds, DUP - 88,346
Maginness, SDLP - 78,489
Nicholson, Ulster Conservative and Unionist - 82,893
Parsley, Alliance - 26,699
Agnew and Parsley eliminated
Sinn Fein's vote is down 0.3% on the last European poll in 2004; the Conservatives and Unionists are up 0.5%; the SDLP has increased its vote by 0.3% and the Green Party is up 2.4%.
BBC Northern Ireland political editor Mark Devenport said there were a number of reasons for the DUP's poor performance.
"The Westminster expenses story and doubts about Diane Dodds' TV performances clearly played into the DUP reversal.
"As the dominant party in the executive they were also always going to be in line to be hit by a protest vote.
"One of the most important factors is that this was the first election since the DUP did its deal with Sinn Fein. They were always going to lose a section of their "never, never, never" support base."
Turnout, confirmed at just below 43%, has fallen dramatically from the last election. It means that 488,891 people in Northern Ireland voted.
There were 4,319 rejected papers and 484,572 valid papers.
Three hundred people counted the papers at the King's Hall in south Belfast.