The Istanbul Metropolitan Municipality said some areas had the highest amount of rain since 1985.
Istanbul was battling to recover from flooding caused by what officials said on Thursday was the heaviest rainfall in the city since records began more than 80 years ago, as the downpour continued.
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The rain began lashing Turkey's largest city in earnest on Wednesday morning and intensified throughout the day, causing chaos and flash flooding, with footage showing cars being dragged away by the fast-flowing waters.
"We are talking here about the highest level of precipitation in Istanbul since records began in 1942," Istanbul governor Davut Gul said.
Two people died in the floods, one of them a 14-year-old boy who was electrocuted when he stepped into a puddle in the Balat area. He was rushed to hospital but medical personnel were unable to save him, officials said.
Another three people were being treated in hospital, Gul said.
On Wednesday evening, the governor said schools would be shut across Istanbul until Monday, urging people to stay home "unless absolutely necessary" and advising those living in basement properties "to spend the night on safer, higher floors".
He advised residents to stay away from "stream beds, underpasses and other areas at risk of flooding".
Dramatic footage posted online and collated by DHA news agency showed a line of parked cars in the northern Sariyer district being pushed into the torrent of muddy water, where they were swept away.
Another showed people being hauled from the raging waters to safety through a first-floor window, while elsewhere two people with umbrellas were seen stepping into the shovel of a large mechanical digger, which took them away.
Forty-three flights bound for Istanbul Airport on the Black Sea had to be diverted, as did three flights heading for the city's Sabiha Gökçen airport on the Asian side, which also temporarily suspended take-offs due to strong winds, the transport ministry said in a statement carried by state news agency Anadolu.
Turkey's AFAD disaster agency has set up a crisis desk to manage incidents caused by the heavy rainfall, which by nightfall Wednesday had risen to 1,277 flooding incidents, 15 landslides, 47 people stranded and two roofs blown off.
The heavy rains are expected to continue over the weekend.