After a hastily-convened meeting with Erdogan, Prime Minister Binali Yildirim said Ala had stepped down and would be replaced by Suleyman Soylu, the current labour and social security minister.
There was no official explanation for why Ala had quit and Turkish media said it was unexpected.
Yildirim thanked Ala "for his services."
The ministerial change follows a failed July 15 coup, which was blamed on supporters of US-based Muslim preacher Fethullah Gulen, an arch enemy of Erdogan.
The abortive putsch raised questions about intelligence failings which government officials have acknowledged.
Ala leaves the post as the insurgency between Turkish security forces and militants from the outlawed Kurdistan Workers' Party (PKK) rages following the collapse of a two-year truce last summer.