Prosecutors launched a probe in December, 2015 over the graphic pictures that the French National Front (FN) leader posted on social media, which included the decapitated body of US journalist James Foley.
"The result is clear, a big majority is in favour of the lifting of immunity," acting parliament speaker Dimitrios Papadimoulis said, after lawmakers in Brussels voted by a show of hands.
French legal sources said the move was expected to become effective in a few days, after the investigating judge receives formal notification of parliament's action against the National Front MEP.
The case concerns only the tweets, and not a separate probe into allegations that Le Pen misused public funds when hiring a parliamentary aide, they said.
The development is the latest twist in France's dramatic presidential election campaign, coming a day after rightwing candidate Francois Fillon vowed to continue his bid for power despite the fact he is to be charged over his own fake jobs scandal.
Le Pen addressed the tweets in 2015 to a French television journalist who had likened her party to the jihadist group.
The images were tweeted with the caption "This is Daesh", an Arabic acronym for the Islamic State group.
They showed Foley's bloodied body with his decapitated head on his torso, as well as a man on fire in a cage, and a victim being driven over by a tank.
Police in the Paris suburb of Nanterre launched an investigation into "the dissemination of violent images".
An investigating judge summoned her for an interview in April 2016 but Le Pen has so far refused to attend, citing her European Parliament immunity.
If found guilty, Le Pen could face up to three years in prison and a fine of 75,000 euros (US$78,800).
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'A political inquiry'
"This lifting of immunity is absolutely ridiculous and problematic," one of Le Pen's top aides, Florian Philippot, told BFM television.
Le Pen herself has dismissed the inquiry as a "political" attempt to derail her presidential bid, in which she is predicted to win the election's first round in April but lose a run-off in May.
"I sent two or three photos of Daesh atrocities and I said 'This is Daesh.' I denounced this atrocity," she told French broadcasters on Thursday, hours ahead of the EU Parliament vote.
"Why investigate me and not others? I am a lawmaker and I was denouncing Daesh in my role as a lawmaker," she added.
"It's a political inquiry."
On Tuesday Le Pen criticised efforts to lift her immunity as "part of the system that wants to stop the French people's candidate that I am."
French police have also opened a probe against Gilbert Collard, a National Front lawmaker in France, who tweeted a similar violent image on the same day.
Last month the French national assembly refused to consider a request to lift his immunity after deciding it was not "sufficiently specific".
Foley, a freelance journalist, was captured in Syria in 2012 and beheaded in August 2014.
His bereaved parents John and Diane said they wanted the images removed immediately, accusing Le Pen in a statement of using the "shamefully uncensored" picture for political ends.
While Le Pen is forecast to finish first in the first round of the election on April 23, her centrist rival Emmanuel Macron is considered the favourite to win a run-off vote on May 7.
