"We have completed the process of removing Irineos as patriarch," patriarchate secretary Aris Tarchos told journalists in East Jerusalem on Saturday.
Irineos left the patriarchate in Jerusalem's Old City on Friday afternoon after two-thirds of the church leadership approved his dismissal.
Saturday's announcement officialises that decision. Irineos I has faced increasing pressure from his largely Arab flock to step down since mid-March, when an Israeli newspaper published details of a multimillion-dollar transaction in which ideologically motivated Jewish business people acquired church land in a predominantly Palestinian area of the Old City.
Although the patriarch repeatedly denied involvement in the sale, his denials fell on deaf ears. Enraged by the move, his mostly Palestinian flock have stopped at nothing to have him removed.
Earlier this week, the ex-financial manager of the patriarchate, who is thought to be behind the land sale, alleged that Irineos sold the properties to win Israel's approval and prove he was not pro-Palestinian.
Nikos Papadimas, who fled Israel to an unknown destination after the scandal erupted, told the Haaretz daily that Irineos "wanted to prove to the Israeli authorities that he did not support the Palestinians and the PLO (Palestine Liberation Organisation)".
The Synod on Friday issued a statement saying Irineos "has been driven by a spirit of falsehood, misunderstanding the meaning of the church (and) irresponsibly handling the property of the patriarchate."
Irineos had "put in danger our rights and our presence in the Holy Places," it concluded. During the night, Irineos returned to the patriarchate, accompanied by a heavy Israeli police escort, where he began packing his belongings, church sources said.
"He walked out of the building after a tumultuous meeting with other church leaders," a source close to the patriarch told reporters on Friday.
The land sales caused anger among
Arab Christians and Muslims
Representatives of the Palestinian Orthodox faithful had earlier welcomed the dismissal, with Dimitri Diliani, leader of a secular group of nationalist Palestinian Christians, insisting that the patriarch be put on trial before a church court.
"Irineos must not be allowed to leave (the country) until he has been investigated and tried before a church court," he told reporters.
"This is an important move; but the battle is not yet over -the fight is now on to retrieve the properties that were leased."
Purchasing property in the Old City, which is in occupied and annexed east Jerusalem, is fraught with political tensions as Jewish groups often try to obtain properties in Palestinian areas in a major settlement drive.