Flash flooding saw main roads turned into rivers, with many soaked commuters forced to abandon submerged vehicles.
Many underpasses, intersections and some metro and bus stops were put out of action, leaving thousands of pedestrians stranded, according to Anadolu Agency reporters around the city.
Drenched commuters could be seen wringing out wet clothes or going barefoot after abandoning sodden footwear.
A metro line running from Ataturk International Airport on the city’s European side was flooded, and similar scenes were recorded at the Avrasya (Eurasia) road tunnel, opened in December 2016.
The city's tram service between the Bagcilar suburb to Kabatas on the banks of the Bosphorus was also suspended.
Many buildings and offices were flooded as swirling waters tore down trees and utility poles. A number of minor traffic accidents have been recorded so far, Anadolu Agency correspondents report.
Transport Minister Ahmet Arslan described the heavy rainfall as a “disaster”. He said it took just 90 minutes of heavy rains to create the “extraordinary situation”.
Despite the disruption, no casualties had been reported, according to Disaster and Emergency Management Authority (AFAD) President Mehmet Halis Bilden:
“They [AFAD teams] have all been carrying out search-and-rescue efforts. Thank God, there are no casualties, according to initial reports.”
Istanbul governorship warned people to leave their vehicles at home where possible, to prevent further road problems.
Istanbul Sea Buses and Fast Ferry Operators (IDO) cancelled some sailings.
According to forecasters there may be no let-up in the rain, with Istanbul expected to see more downfalls in the afternoon, continuing until evening, together with strong wind.
Istanbul Governor Vasip Sahin said more rain was expected at 2 p.m. local time (1100GMT).