He was seen surrounded by supporters, and said the coup attempt was an "act of treason" in a live TV speech.
Forty-two people died during overnight clashes in the capital, Ankara, most of them civilians, the prosecutor's office said.
Prime Minister Binali Yildirim said the situation was largely under control and 130 people had so far been arrested.
He has ordered the military to shoot down aircraft being used by coup plotters.
Earlier, one of the helicopters being flown by forces involved in the coup attempt was shot down over Ankara.
However, the whereabouts of the military chief of staff remains unknown and sporadic gunfire is still reported in major cities.
Istanbul's main Ataturk airport is now under army control, and flights - which had been interrupted for some hours - are due to resume from 06:00 (03:00 GMT).
Soldiers were earlier seen at strategic points in Istanbul, with jets flying low in Ankara.
Two large explosion were also heard near Istanbul's central Taksim Square.
There were also reports of blasts at parliament building in Ankara. MPs were believed to be hiding in shelters.
Broadcaster CNN Turk was reportedly taken over by soldiers, and its live broadcast was cut.
In Washington, US President Barack Obama urged all parties in Turkey to support the "democratically elected government".
Nato called for "full respect" for Turkey's democratic institutions.
'Parallel structure'
Speaking in Istanbul in the early hours on Saturday, President Erdogan promised to clean up the army.
"Those who drive around in tanks will have to go back to where they came from," he said.
He also dismissed the coup leaders as "terrorists".
Mr Erdogan earlier told CNN Turk by mobile phone the action was by a "parallel structure" that would bring the necessary response. He has used this term in the past to refer to Fethullah Gulen, a US-based Muslim cleric he accuses of fomenting unrest.
Fethullah Gulen: Powerful but reclusive Turkish cleric
Mr Erdogan had called on people to take to the streets to oppose the uprising.
He said: "I urge the Turkish people to convene at public squares and airports. I never believed in a power higher than the power of the people."
The president said he had returned to Istanbul from the holiday resort of Marmaris in the south-west of the country. He said the town was later bombed,
Defying the announced curfew, a number of Erdogan supporters turned out on Taksim Square in Istanbul late on Friday.
There were reports of clashes there, with some on Twitter saying that gunfire had been heard near the square.
After the military takeover was announced, a statement from the group was read out on national broadcaster TRT. It said that the democratic and secular rule of law had been eroded by the current government. There would be new constitution, it said.
The statement declared that a "peace council" now ran the country and there would be a curfew and martial law.
There were reports Turkey's top general, General Hulusi Akar, was among those taken hostage at the military HQ.
Mr Yildirim told NTV by telephone: "There was an illegal act by a group within the military that was acting out of the chain of military command. Our people should know that we will not allow any activity that would harm democracy."
Traffic was stopped from crossing both the Bosphorus and Fatih Sultan Mehmet bridges in Istanbul.
Source: BBC
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