Irineos returned to his living quarters in Jerusalem's Old City before dawn on Saturday, hours after senior church officials said they had voted to dismiss him for his alleged role in a controversial property deal.
However, other clergymen said Friday's decision was not valid.
The patriarch can only be ousted by the 17-member Synod, the church's highest decision-making body.
The patriarch's supporters said only he could convene the Synod and that Friday's vote among top clergy, including members of the Synod, was held without the patriarch having called the meeting.
Rebel clergy said they had decided to dismiss Irineos because of allegations he was involved in leasing church property to Jewish settlement groups in east Jerusalem, the sector claimed by the Palestinians as a future capital.
A church spokesman, Archmandrite Atallah Hannah, said an acting patriarch would be elected next week.
Rebels accuse the patriarch of
playing a role in the property sale
However, another clergyman, Archmandrite Milinios Bassal, said that only Jordan's attorney general could decide whether Friday's decision was valid and that until he has done so the patriarch remains in charge.
The church complies with a 1958 Jordanian law that bans any sale of church land and property. Jordan ruled east Jerusalem and the West Bank until Israel seized the territories in the 1967 Middle East War. Israel has since annexed east Jerusalem.
Jordan renounced its claims to east Jerusalem in 1988, but maintains custody of holy shrines there.
On Thursday, Jordan said it would accept the dismissal of the patriarch if two-thirds of Synod members back the decision. It was not clear how much support each side has in the Synod.
Palestinians President Mahmoud Abbas said the Palestinians were holding discussions with their Jordanian counterparts on whether to accept the rebel clergy decision and withdraw recognition from Irineos. Church tradition holds that the ruling powers in the region must approve the church leader.
Palestinians are furious because
the deal aids Jewish settlers
Hannah said Synod representatives were to meet later on Saturday with officials of the Palestinian Authority and the Jordanian government to brief them on the decision to dismiss the patriarch.
The property transactions Irineos allegedly was involved in are politically explosive because Palestinians see them as abetting Jewish settlement groups in their efforts to expand their presence in east Jerusalem. Most of the church's flock in the Holy Land are Palestinians.
Bassal said Irineos was determined to fight the dismissal, telling his supporters that accepting it would be tantamount to admitting involvement in the land deal.
Irineos has denied allegations that he was involved in leasing church property, including two hotels in the Old City, to an Israeli firm.
At a rare news conference last month, Irineos said he was unaware of the alleged transactions and said he was not involved in any deal that reportedly was signed by Nikos Papadimas, the church financial officer who vanished three months ago.
Papadimas is wanted in Greece after Greek Orthodox Church officials in Athens accused him of fleeing with $800,000 in church funds. His wife is wanted on separate charges of money laundering. Separately, a European arrest warrant has been issued for Papadimas, Greek officials said.