80-year-old Le Pen, as the most elderly member, would have been able to take role on 14 July, however, after the alteration to the rules it will go instead to the outgoing president of the assembly.
Mr Le Pen has sparked much criticism in the past when, in 1987, he had referred to the Nazi gas chambers as "a detail of history".
As the leader of the French National Front (FN), Le Pen is a political candidate hoping for re-election in the European Parliament elections on 4-7 June.
The head of the French conservative party supported the Socialists and Greens in their bid to prevent Mr Le Pen from chairing the assembly.
Mr Le Pen's claim about the Holocaust victims caused him to be given a fine of 1.2m francs, as well as sparking much outrage over his remarks.
