Kykkos Bishop Nikiforos said on Wednesday the Holy Synod's decision, a first for the Cyprus church, was unanimous.
The case shocked the conservative east-Mediterranean island nation after the 29-year-old victim was found dead in her home last month.
Many were outraged when local media revealed that the priest kept his job after a criminal court jailed him in 2013 for the same crime, which took place in the 1990s.
His conviction was upheld on appeal.
The priest, who can appeal against the church decision, denied wrongdoing.
Orthodox priests are allowed to marry.
Bishop Nikiforos said the church will act to avoid delays in handling such issues in the future.
Reporting by Associated Press.
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