The populist far-right leader, first elected to the European Parliament in 2004, said ahead of the vote that she was a "dissident" and had invoked her right to freedom of expression. Le Pen said she was confident she would win any trial.
Prosecutors in Lyon in central France are investigating Le Pen for alleged incitement to racial hatred over the remarks, which she is said to have made during a speech in 2010.
In the speech she denounced the holding of Muslim prayers in the streets of France -- where a dearth of mosques has forced many to pray outside -- saying: "For those who like to talk about World War II, to talk about occupation, we could talk about, for once, the occupation of our territory."
"There are no armoured vehicles, no soldiers, but it is an occupation all the same and it weighs on people."
First elected to the European Parliament in 2004, she won 18 percent of the vote in the first round of France's presidential election in April 2012, the party's highest-ever score. The Parliament's judicial committee last month voted with an overwhelming majority in favour of lifting Le Pen's immunity -- a vote that French lawmakers abstained from to avoid any accusation of a political settling of scores.
FN vice president Florian Philippot reportedly said last month that it would be unheard of if Le Pen lost her immunity "for having spoken the truth about the (Muslim) prayers in the streets which still take place.... The French do not like when people hide the truth from them."
As with many national parliaments, members of the European Parliament enjoy immunity from criminal and civil liability for opinions expressed as part of their duties, unless the chamber votes to lift the immunity. Immunity has been revoked dozens of times for MEPs in the past.
Le Pen's father, Jean-Marie Le Pen, had his European Parliament immunity revoked in 1998 when he said that Nazi gas chambers were "a detail" in the history of World War II. Jean-Marie Le Pen has several convictions for racism and anti-Semitism.
He and his daughter were both in the chamber during Tuesday's vote, along with the third National Front member of the European Parliament, Bruno Gollnisch. The independent watchdog site VoteWatch Europe said Marine Le Pen is one of the least active European lawmakers.
She has never authored any report or resolution and her public speeches in the chamber are extremely rare. With a year to go before the next European elections, the National Front is neck and neck with the French Socialist party and the centre-right UMP with 21 percent of voting intentions, according to a survey by the Ifop polling agency.
By Guylain Gustave Moke