"I have lately found myself in difficult moral and professional controversies with the Prime Minister, a number of other ministers, and some members of Knesset," Ya'alon said at a Tel Aviv press conference after his announcement.
"To my great sorrow, they have taken over Israel, and the Likud movement, dangerous and extremist elements, that upend the house and threaten it. This is not the Likud movement that I joined."
Ya'alon has been in a protracted public argument with Prime Minister Benjamin Netanyahu over the Israeli military. In recent weeks, Ya'alon has encouraged military generals to speak out about moral issues and the rules of engagement, even if they did not have the support of politicians. The statement was seen as criticism of Netanyahu.
The two men met for an hour Monday to reconcile their differences, saying, "There is no quarrel."
Ya'alon resigned within the week.
Netanyahu issued a statement lamenting Ya'alon's resignation. "I am sorry about the decision of 'Bogie' Ya'alon. I believe that he needed to stay as a full partner in the leadership of the state in the position of foreign minister," Netanyahu said, referring to the post Ya'alon was offered instead of defense minister.
"I would like to thank him for years of service in the Israel Defense Forces (IDF) and the defense establishment. The allocation of portfolios did not emerge from a fallout of trust between us. It emerged from the need to widen the government in order to bring stability to the State of Israel as it faces significant challenges before it."
Ya'alon is set to be replaced by controversial right-wing politician Avigdor Liberman, who leads the Yisrael Beiteinu party. Netanyahu's Likud party has been in negotiations to expand his narrow 61-seat coalition in the Knesset
, Israel's parliament, by bringing Yisrael Beiteinu into the government.
Liberman, one of the most polarizing figures in Israeli politics, has expressed some hawkish and even extreme views in the past. In 2001, he said he would bomb Egypt's Aswan Dam in the event of war between Israel and Egypt. He advocates populated territory swaps in any final status agreement between Israel and a future Palestinian state, exchanging Jewish settlements in the West Bank for Arab-Israeli towns within Israel.
Hanan Ashrawi, PLO Executive Committee member, harshly criticized the addition of Yisrael Beiteinu to the government. "Such a decision is extremely dangerous -- Liberman, who has called for the beheading of Palestinians and for their transfer outside the state of Israel, is a serious threat to peace and stability, and his appointment will generate a culture of lawlessness, extremism, violence, and hate in Israel."
Yehuda Glick, a Temple Mount activist and Likud party member, is set to take Ya'alon's place in the Knesset. The right-wing activist has called on Jews to pray at one of Jerusalem's holiest sites, known to Muslims as al-Haram al-Sharif, or the Noble Sanctuary, and to Jews as the Temple Mount
. Under the status quo agreement between Israel and Jordan, only Muslims are allowed to pray at the holy site.
In October 2014, Glick was shot in the upper body after leaving a conference called "The Jewish People Return to the Temple Mount."