MEPs voted by 447 votes to 196 to strip Czarnecki, of Poland's ruling nationalist Law and Justice (PiS) party, of the largely ceremonial office for "serious misconduct".
Czarnecki, 55, last month branded MEP Roza Thun a "szmalcownik" -- an insult referring to Polish collaborators during World War II who handed over Jews to the Nazis for money.
Czarnecki, who is one of 14 European Parliament vice presidents, then refused to apologise during a radio interview.
In January, heads of the main political groups wrote to the parliament president Antonio Tajani to "denounce an unacceptable and degrading declaration" and ask for sanctions for "this deplorable attitude".
The spat comes in the midst of an ongoing crisis between the EU and the PiS-led government in Warsaw over highly controversial judicial reforms which Brussels says threaten the rule of law.
The EU has threatened to impose unprecedented sanctions that could strip the Polish government of its voting rights in Brussels.
"It's good that so many people are shocked, we cannot tolerate that," Thun told AFP, who had criticised the nationalist policy of the current Polish government on Franco-German broadcaster Arte.
Czarnecki remains a member of parliament and a new vice president must now be chosen from his European Conservatives and Reformists political group, which also includes Britain's ruling Conservative party.
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