The patriarch has been under attack over a deal in which church property in Jerusalem was leased to a Jewish group.
Such land transactions, while legal, are politically explosive because Palestinians see them as abetting Jews in their efforts to expand their presence in occupied east Jerusalem.
Palestinians consider that sector of the city as capital of their future state, while Jews claim the entire city as their eternal capital.
The church leadership announced on Thursday it was ending all contact with Irineos because of corruption suspicions and considers him dismissed. That decision, however, was non-binding.
In their statement on Thursday, the rebel clergy accused Irineos of being "incorrigibly caught up in a syndrome of lying, religious distortion, degradation of the patriarchate's role, and irresponsible mishandling of patriarchate property".
On Friday, the Synod officially endorsed the position and Irineos left the patriarchy, church spokesman Attalah Hanah said.
"We decided to fire him and he left today and we don't know where he went," Hanah said.
Irineos, who has denied the allegations, had been under pressure to resign since March when an Israeli newspaper reported that the church had leased property, including two hotels, to an Israeli firm. The sales would bolster the Jewish presence in east Jerusalem, a traditionally Arab quarter.
Palestinian officials said the church leaders were meeting to begin the process of electing a new patriarch.
"We know that a majority of the Holy Synod met today and decided to dismiss the patriarch and according to the law they have the right to do so," said Emil Jarjour, who heads a Palestinian ministerial committee investigating the land deal.
"Now they are taking the necessary steps to conduct elections in the near future to choose a new patriarch," he said.
A Palestinian Christian holds up a
banner calling for his resignation
It was not clear where Irineos went after the Synod meeting. Church officials said he left with an escort of Israeli police, however police denied this.
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.