The storm, which lasted about 20 minutes, paralysed traffic and caused flash floods that submerged cars in some streets, according to pictures on social media.
Sixteen planes which had been heading to the city's Ataturk airport were routed to other destinations, the pro-government Anadolu news agency reported.
City hall said more than 7,000 people had been mobilised to deal with the aftermath of the storm.
Around 230 trees were uprooted, nearly 90 roofs collapsed and a number of fires broke out but were quickly extinguished, it said in a statement.
Further storms were possible in the night, it added.
The incident occurred just nine days after Istanbul was pounded by heavy rains and winds of up to 80 kilometres (50 miles) per hour, flooding streets and metro stations and disrupting tram lines, but without causing casualties.
The municipality said on average 65 millimetres (2.5 inches) of rain fell on July 18 while the district of Silivri experienced as much as 128 millimetres.
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