Ms Le Pen is under investigation in France for posting three graphic images of IS killings in 2015, including the beheading of US journalist James Foley.
Her position as an MEP has so far meant she could not be prosecuted.
Ms Le Pen is currently running to be French president.
Opinion polls suggest she is on course to win the first round in April, but centrist Emmanuel Macron is gaining ground and looks likely to beat her in a second round in May.
A Figaro/LCI poll on Sunday put Mr Macron - who was unveiling his manifesto at the same time as it was revealed Ms Le Pen had lost her immunity - on 58% in the run-off, against 42% for Ms Le Pen.
The European Parliament vote - carried by a "big majority", according to acting parliament speaker Dimitrios Papadimoulis - confirmed a preliminary decision taken on Tuesday by the legal affairs committee of the European Union legislature.
Ms Le Pen had dismissed efforts to lift her immunity as "part of the system that wants to stop the French people's candidate that I am".
The allegations date back to December 2015, when she tweeted the pictures in response to a journalist who drew an analogy between her anti-immigration Front National (FN) party and IS extremists.
Mr Foley's parents accused Le Pen of using the "shamefully uncensored" image of their son for her own political ends.
However, the vote only lifts her immunity in this particular case and will not cover a separate investigation into whether the FN misused European Parliament funds.
Ms Le Pen has refused to attend a police interview over the latter allegations. She denies wrongdoing and claims that they are a plot to derail her campaign.
Le Pen in trouble - again
Kevin Connolly, BBC News, Brussels
This is not the first time Marine Le Pen has found herself in legal hot water at the European Parliament.
Her immunity was lifted four years ago to facilitate an investigation into remarks she made about Muslims praying in public in France - and she's locked in a long-running dispute about an alleged misuse of parliamentary expenses.
This latest case involves her spreading images of brutal IS executions on social media.
In theory such actions can result in a heavy fine or even imprisonment in France although Madame Le Pen may calculate that this is an issue that will do her no harm with hard-right supporters of her party, the Front National. No charges were brought against her the last time her immunity was lifted.
With her conservative rival Francois Fillon facing an investigation into his family's use of parliamentary salaries and expenses, Thursday's decision leaves France in the unusual position of having two prominent candidates for the presidency facing the prospect of criminal prosecution.