Police defused the second bomb thrown on the grounds of the Turkish Orthodox Ayayani Church in downtown Istanbul late Friday, the Anatolia news agency reported.
A third bomb, found in a plastic bag at a school run by the Ecumenical Orthodox Patriarchate, was also defused.
The attack comes on the eve of Easter celebrations for Orthodox Christians and prompted police to increase security around churches throughout the city, Anatolia said.
There were no immediate claims of responsibility for the explosion, which damaged the church's back door and a car that was parked nearby. Police in Istanbul refused to comment on the attack.
Orthodox churches, however, have come under attack before.
In 1998, a priest was injured by a bomb thrown at the Ecumenical Patriarchate, home of Patriarch Bartholomew I, the spiritual leader of the world's more than 300 million Orthodox Christians. That same year, assailants also killed an elderly chapel caretaker.
Suspicion fell on radical Islamic groups who accuse Bartholomew of trying to create an Orthodox state on Turkish soil. Several militant Islamic groups are active in Istanbul.
The small Turkish Orthodox Church does not recognize Bartholomew's ecumenical status.