The downpour began in the city's northern region at around 9 pm local time (1800 GMT) on Tuesday, Xinhua reported.
The governor's office said a Guinean national died in the Basaksehir district, and a Turkish citizen was killed in the Kucukcekmece district. The injured were treated in hospitals.
The office said that the flash floods damaged thousands of houses and shops, and some people remained stranded.
It added that the evacuated would stay in government guesthouses and dorms. Two hospitals partially affected by the rains continue to admit patients.
Northwestern Turkey has been under heavy rainfall since Tuesday morning. According to the state-run Anadolu news agency, the death toll in the floods in the Kirklareli province has risen to three.