Several major roads were flooded, prompting official warnings.
"As the rain continues to pour in most parts of the country, motorists are advised to be cautious," the interior ministry tweeted after earlier calling the rainfall "medium to heavy".
Some apartment buildings on the Pearl Qatar, an artificial island in Doha, estimated to have cost USD 15 billion (13.5 billion euros) to build, suffered flooding, as did the nearby suburb of Qanat Quartier, built to resemble Venice.
The Peninsula English-language newspaper reported that rain caused leaks at major Doha shopping centre the Landmark Mall.
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Many people used social media to post videos and pictures, with some questioning how a relatively small amount of rain - the first of the winter - could cause such problems.
The wet weather had been predicted and the government "Rain Emergency Team" had already convened to discuss potential problems.
Last November, the government began an inquiry after rain damaged Doha's Hamad international airport, which opened in 2014, flooded roads and streets and caused some schools to close.
World Bank figures show Qatar's average annual rainfall is around 75 millimetres.
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