Mr McMillan-Scott said the Tories were being "exploited" for political ends
The Conservative MEP Edward McMillan-Scott has been expelled from the party.
The MEP was suspended in July after he stood for vice-president of the European Parliament in defiance of party instructions.
He was criticised for challenging a Polish MEP, one of the Tories' new allies in Brussels, for the role.
The Conservatives said they were "disappointed" by the MEP's behaviour but Mr McMillan-Scott, who once led the Tory group in Brussels, is to appeal.
He said he would not be made a "scapegoat" for widespread criticism of the Conservatives' decision to forge a new alliance in Brussels after June's elections.
David Cameron pulled the Tories out of the centre-right group of MEPs, where they sat alongside governing parties in Germany, Italy and France, saying he did not share its federalist views.
He re-aligned them within the European Conservatives and Reformist Party group, made up of parties from central and eastern Europe, including Poland and the Czech Republic.
Opposition parties said this put the Tories on the fringe of Europe but the Conservatives said the move was good for democracy and it would continue to work with other groups in the Parliament.
Mr McMillan-Scott, who was unhappy with this decision, chose to stand against Polish MEP Michal Kaminski, a member of the new coalition, for the role of vice-president.
He won the contest, defeating Mr Kaminski in the process.
Mr McMillan-Scott said Mr Kaminski was "inappropriate and unsuitable" for the role because of reported past links with extreme, far right groups, something Mr Kaminski denies.
"I will not be a scapegoat for this," Mr McMillan-Scott said of the decision to expel him, one he said he was not consulted on.
"David Cameron has been exploited by those in the party who want Britain to leave Europe. I want Britain to lead in Europe."
The Conservative leadership said it had written to the MEP outlining the steps he would need to take to have the whip restored, including resigning the post of vice president, and the penalties for not doing so.
"He failed to respond to any of these conditions and therefore his membership of the party has been revoked," a spokesman said.
Other Tory MEPs said Mr McMillan-Scott's position had become untenable.
"I am disappointed in him and the party is not to blame," said Timothy Kirkhope, the party's leader in Brussels.
"This was not so much about his views but about his behaviour. I can imagine that he will come under pressure to stand down as does any member of the Parliament that crosses the floor."
Labour said the expulsion showed the Tories were "falling apart" over Europe and that moderate pro-Europeans no longer had a place in the party.