Metropolitan Theofilos was elected by the church's Holy Synod in a 14-0 vote.
Church rebels had dismissed Patriarch Irineos I earlier this year over its leasing of prime property in east Jerusalem to groups interested in expanding the Jewish presence there. The long-term leases enraged the church's predominantly Palestinian flock, which claims east Jerusalem as the capital of a future state.
World Orthodox leaders stopped recognizing Irineos' authority in May, but he continued to resist demands to step aside, saying a former aide signed the leases without his knowledge. Irineos wasn't immediately available for comment Monday on the election of his successor.
Atalla Hana, a senior cleric at the Jerusalem church, said Theofilos "vowed yesterday and today before the synod and the religious men of the church to return all the properties that were leased to Israelis."
Greek media have reported that Theofilos, the metropolitan of Tabor in Galilee, had served previously as a Greek Orthodox Church envoy in Qatar. He reportedly has close ties to the Greek Orthodox leadership in the United States.
Theofilos also apparently has support from clerics still loyal to Irineos, which could have helped bolster his credentials as a compromise successor.
Dozens of worshippers shouted their approval after the vote by the synod in the Church of the Holy Sepulcher, Christianity's holiest shrine in Jerusalem.
Under church law, any new patriarch must be approved by the three governments under whose jurisdiction the church's flock lives. The Palestinian Authority and Jordan have recognized Irineos' dismissal, but Israel has not.
Israeli government officials said they had not yet adopted a position regarding the election of Theofilos. Israel has previously said it would not work with Irineos' replacement.
Asked what the church would do if Israel refused to do business with Theofilos, Hana said the church was not interested in Israel's position on the new patriarch.
Jordanian lawmaker Audeh Quwas, who was closely involved in investigating the Irineos affair, said Jordan's approval of Theofilos' election was all but assured.
"It is only protocol that Jordan's blessing must be given for completion of the process," Quwas told The Associated Press.
He called on the new patriarch "to reverse the mistakes of Irineos, and this means going to court" to overturn the property leases, Quwas said.