Despite earlier misgivings, the assembly delivered a landslide vote in favour of Mr Santer, with 416 out of the 578 MEPs present voting in favour. However, several British MEPs voted against, including the Conservative group's chief whip.
The appointment must now be confirmed by member states before the new Commission is sworn in by the European Court of Justice, in Luxembourg.
Mr Santer and his Commission have had to run the gauntlet as never before in the Parliament, because of the new right of the assembly to give or withhold its assent. The procedure was intended to underpin the democratic credentials of the Commission while increasing the power of the Parliament.
Mr Santer said there were two winners: the Commission, whose legitimacy had been increased; and the Parliament. "They have imposed their choice and won a number of concessions."
He did not disguise his relief that the proceedings were over. "It has been a lengthy debate and it has indeed been a painful process for some people.''
One hundred and three MEPs voted against Mr Santer, mainly the Communists, extreme right wing and the Greens. Winnie Ewing and Allan Macartney, of the Scottish National Party, were both amongst the nay-sayers, as were Giles Chichester, Graham Mather, James Provan and Edward Kellet-Bowman of the Conservatives and Alex Falconer, Carol Tongue and Bill Miller of the Labour Party.
Mr Provan is the Euro-Conservatives' chief whip, and the group had decided yesterday morning that it would vote for Mr Santer. Mr Mather and Mr Chichester are both Euro-sceptics. Mr Falconer was a leading member of the group of Labour MEPs who signed a petition protesting against the dropping of Clause IV. The motion thus put British MEPs of different persuasions voting together.
Fifty-nine MEPs abstained, amongst them Ken Collins, chairman of the environment committee, who had expressed severe doubts about Ritt Bjerrgaard, the new Danish environment commissioner. She had been alleged to have said that the assembly was "not a real Parliament", though Mr Santer and other witnesses said the quote was taken out of context.
Another with some egg on his face was Padraig Flynn, the commissioner for social policy, who had been accused of a lack of commitment to sex equality. However, Irish officials said that the affair had, if anything, improved Mr Flynn's position in Irelandsince he was felt to have been unfairly singled-out.
The vote was never really in doubt, though the leader of the Socialist party, Pauline Green, had said that her party would block the appointment of the Santer Commission without significant concessions.
In the event, Mr Santer massaged some of the portfolios, taking control of some key issues himself. He also committed himself to reconsidering a code of conduct that regulates the way the Parliament and Commission work together. This could give the Parliament some limited added weight, a useful concession in the run-up to 1996 when EU leaders meet to reconsider the Maastricht treaty.
Mr Santer has emerged rather ruffled from the event, but with his Commission intact. The Parliament can pat itself on the back for having achieved some concessions.
But leading parliamentarians had threatened to topple Mr Santer and then rowed back, helping to underpin the Parliament's reputation for marching up to the top of the hill and then going back down again. Last year, the Socialist group pledged itself to vote against Mr Santer but party indiscipline ensured the threat was hollow.