Streets transformed into rivers and squares turned into lakes on the island in southern Italy on Tuesday.
Rescuers said at least two people have died due to the extreme weather which has caused a blackout in the city centre and flooded shops.
Schools have been closed in the city and in a number of nearby towns.
On Monday, a 67-year-old man died after his car was hit by rising waters and mud. His wife was still missing.
The body of a second man was discovered under a car amid torrential rains sweeping the town of Gravina, north of Catania, according to the Misericordia group of volunteers who are helping police and firefighters.
Police confirmed the death without providing any further details.
“I urge all people not to leave their homes except for emergencies,” Mayor Salvo Pogliese wrote on Facebook.
He ordered the closure of all shops, apart from pharmacies and groceries, until midnight in the announcement.
The rain has inundated some of Catania’s most famous streets and squares.
Floods also hit a ward at Catania’s Garibaldi hospital, according to media reports.
“The emergency situation is widespread and extremely critical and it does not seem to be improving,” a fire brigade spokesperson said.
Parts of Sicily and the adjacent toe of Italy, Calabria, were being pounded by a rare tropical-like cyclone known as a medicane, according to forecasters.
The sea was eight degrees warmer than the average for this time of year with the storm expected to peak between Thursday and Friday, reports show.