The prayers were held in 2,000 mosques across the Muslim country of 35 million people.
"We never had such prayers before," 63-year-old faithful Abdurashid Rasulov told AFP at a prayer in the capital Tashkent.
"But now, since the rain is delayed, our religious leaders instructed us to ask Allah for rain," he added.
Anvar Abduazizov, 67, said: "We prayed for a blessing for our country and our land and for the rain to pour down abundantly."
For Tashkent, the largest city in Central Asia, this year's drought has been one of the harshest in 170 years, Uzbekistan's Meteorological Agency said this month.
Over the past 60 years, temperatures in Uzbekistan have risen "nearly three times the global average, leading to more frequent droughts", according to a United Nations report.
Climate change is speeding up the melting of glaciers, a key water source for the approximately 80 million inhabitants of Central Asia, a region comprising five former Soviet republics where economies and population are growing rapidly.
The UN and scientists have warned glaciers may disappear by the end of the century.
Increased levels of dust, widespread use of coal for heating and poor quality gasoline for vehicles have meanwhile made Uzbekistan one of the world's most polluted countries.
Uzbek authorities say they have used rain-making technology, but it is expensive and far from being widely implemented.
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