Thousands of other Muslim faithful came from across Turkey and quickly filled specially-designated areas outside of the Byzantine era monument to join in the inaugural prayers.
Many others were turned away, while Orthodox Christian church leaders in Greece and the United States announced a “day of mourning” over Hagia Sophia’s return as a mosque.
The prayers began with Mr Erdogan reciting from the Koran. The head of Turkey’s religious authority, Ali Erbas, led the ceremony and prayed that Muslims would never again be “denied” the right to worship at the internationally celebrated sixth century structure.
As many as many as 350,000 people took part in Friday’s prayers, the president said.
Adem Yilmaz, who attended the prayers, expressed joy at experiencing “the making of history”.
“This turned into a place where all hearts beat at once,” he said.
Brushing aside international criticism, Mr Erdogan issued a decree restoring the building as a mosque earlier this month, shortly after a Turkish high court ruled that the Hagia Sophia had been illegally made into a museum more than eight decades ago.
The structure, a Unesco World Heritage site, has since been renamed “The Grand Hagia Sophia Mosque”.
The move sparked dismay in Greece, the United States and among Christian church leaders who had called on Mr Erdogan to maintain Hagia Sophia as a museum in recognition of Istanbul’s multi-faith heritage and the structure’s status as a symbol of Christian and Muslim unity.
The reopening of Hagia Sophia as a mosque threatens to deepen Turkey’s isolation on the world stage following its military interventions in Syria and Iraq and amid international disputes over oil-and-gas rights in the eastern Mediterranean Sea.
The decision was in line with Mr Erdogan’s ambitions to raise Islam’s profile in Turkey and to make his country a leader nation in the Islamic world.
Hagia Sophia’s re-emergence as a mosque is also being interpreted as a move aimed at consolidating Mr Erdogan’s conservative and religious support base at a time when his popularity is sagging amid an economic downturn.
Built by the Byzantine Emperor Justinian in 537, Hagia Sophia was turned into a mosque with the 1453 Ottoman conquest of Istanbul.
Mustafa Kemal Ataturk, the founding leader of the secular Turkish republic converted the structure into a museum in 1934.
