Melih Gokcek, a staunch Erdogan loyalist who had been in charge of the Turkish capital for 23 years, said he was acting in the country's best interests.
"I leave my post of mayor on orders from our leader Recep Tayyip Erdogan," Gokcek, a member of the ruling Justice and Developement Party (AKP), said in a televised speech.
"I bow to the request of Recep Tayyip Erdogan, not because I do not think I have been successful, not because I think I'm tired... but only because I think (Erdogan) can make our country a leader."
Erdogan co-founded the AKP as an Islamic-rooted party that also aimed to modernise the economy and push ahead with Turkey's EU membership bid.
Erdogan has repeatedly made clear that the party needs to make "sweeping changes" ahead of the 2019 elections, after it showed signs of weakness at the ballot box.
He said in August that "successful" colleagues -- including MPs, mayors and regional party officials -- would be able to stay in their jobs but those showing "tiredness and weariness" would have to move on.
Several mayors have since resigned, including Istanbul mayor Kadir Topbas who stepped down last month after 13 years in the key post.
While the AKP has never been defeated at the ballot box since first winning power in 2002, there have been signs its grip on power has grown slightly less tight in recent years.
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