The replacement to be elected on Thursday will take the patriarch's duties until a new leader is elected, synod secretary Father Dimitrios said.
He said he did not know when a new permanent patriarch would be chosen.
World Orthodox leaders voted in Istanbul on Tuesday to stop recognising the patriarch, Irineos I, who has become embroiled in allegations of leasing church property in east Jerusalem to Jewish investors.
Irineos returned to Jerusalem early on Wednesday from the Istanbul meeting and concealed himself inside his home in the patriarchate compound, Father Dimitrios said.
Irineos did not enter church offices and has not met anyone in Jerusalem since his return, Dimitrios added.
"He has no authority, no power, nothing," Dimitrios said, when asked how clerics in Jerusalem would react if Irineos attempted to conduct church business. "It means nothing to us."
Several weeks ago, church leaders in Jerusalem announced that they considered Irineos dismissed.
"He has no authority, no power, nothing"
The clerics who met in Istanbul on Tuesday did not have the authority to oust him, but by refusing to recognise him have heated up the pressure on him to step down.
The leasing of east Jerusalem property to Jews is a politically explosive issue because Palestinians consider east Jerusalem as the capital of their future state and see an expanded Jewish presence there as challenging that claim.