Tawfiq Okasha hosted Israeli ambassador Haim Koren last week, sparking outrage in parliament where one lawmaker hit him with a shoe -- an insult in the Arab world.
Okasha talked about the meeting in an interview in the Al-Masry Al-Youm daily, saying the two agreed Israel "has a key role in the issue of the dam" being built by Ethiopia on the Blue Nile.
The parliament's official website said 465 deputies -- or more than two-thirds of its members -- voted to deprive Tewfiq of his seat on Wednesday.
"The penalty is not over his meeting with the ambassador of a foreign country, but because of the issues discussed during this meeting, in relation to Egypt's national security," it said.
The issue of the Ethiopian dam is seen in Cairo as a matter of national security.
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"He has failed in his duties by inviting a foreign state to interfere to solve the issue of the dam," deputy Khaled Youssef told AFP.
In a video posted on Facebook, the Israeli ambassador sought to explain the significance of the talks.
"We have to accept differing opinions, to consolidate ties between the two peoples; economic, cultural and social," said Koren.
Although Egypt became the first Arab country to sign a peace treaty with Israel in 1979, their ties have been formally cold over Israel's policies towards the Palestinians.
Egypt's political elite remains hostile to any normalisation of ties with Israel.
Relations between the two further soured after the June 2012 election of the Muslim Brotherhood's Mohamed Morsi as Egyptian president.
The Israeli embassy described the February 24 meeting between Okasha and Koren as "successful", saying "the two parties agreed on staying in touch and pursuing cooperation".