"The intensity of the storm was unexpected," said Rome Mayor Gianni Alemanno, who also activated a toll-free emergency hotline for people to report emergencies and request information.
The heavy rainfall flooded basements across Rome, drowning an elderly man in his below-ground apartment, the Italian news agency ANSA reported.
Another elderly person was reported missing after the storm.
Road traffic was congested as floodwater flowed down streets and blocked passageways.
Train lines into the city experienced delays and closures, as did some underground metro stations in the city.