In Sunday's opening ceremony, Turkish President Recep Tayyip Erdogan said the 120-year-old Sveti Stefan Church remained the "single example" of a church built on an iron skeleton.
The cross-shaped Bulgarian church was built on the banks of Istanbul's Golden Horn in 1898 with 500 tons of prefabricated iron components shipped from Austria. Its restoration since 2011 cost an estimated £2.6 million.
Mr Erdogan said the church contributed to the "beauty and wealth of Istanbul" and was the latest example of Turkey's efforts to restore synagogues, chapels and churches.
Bulgarian Prime Minister Boyko Borisov said his country would work to "normalise and improve" Turkey-European Union relations as his country assumed the EU's presidency.