Fire services said they received at least 10 calls from motorists whose vehicles were stranded when roads became rivers after storms in the upscale districts of Maroussi and Ekali.
A civil defence spokesperson said "dozens of cars were stuck on several main roads" after the early afternoon downpour, adding that traffic was gradually returning to normal.
Firefighters said around 160 residents were briefly trapped in their homes due to the flooding.
Rescuers search fire-devastated Greek areas as toll hits 81
Some rain fell on the coastal region of Mati, 25 kilometres east of the capital, where more than 80 people lost their lives on Monday night when wildfires tore through homes and hotels.
The defence ministry said the army had been called in to remove debris and dig drainage channels to prevent flooding in the fire-ravaged area.
The region around Athens in November saw 16 people killed in flash floods.
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