Tourists and residents of Venice donned high boots to navigate the city streets after strong winds raised the water level over 5 feet before receding.
Two young people died south of Rome when a tree hit their vehicle, while another person was killed in the nearby town of Terracina as winds brought down scores of pine trees.
Six people died on Monday as trees were brought crashing down and rivers were left dangerously swollen.
Tourists were barred from St Mark's Square as local authorities said the "acqua alta" (high water) peaked at 156 centimetres (61 inches).
The victims also included a woman who was buried by mud when a landslide invaded her home near Trento in northern Italy and a man who was slammed against rocks while wind surfing in Emilia-Romagna.
Meanwhile, the Italian Civil Protection Agency said Tuesday that the death toll from the fierce storms battering Italy rose to 11. The waters have only topped 150cm (4ft 11in) five times since records began, adds The Daily Telegraph. Several local authorities shut schools and urged people not to travel unless necessary.
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Venice Mayor Luigi Brugnaro said the city's underwater barriers, now still under construction, would have prevented the flooding had they been completed, reports ABC News.
The lagoon city's St. Mark's Square remained under water for a second day while the adjacent St. Mark's Basilica was also inundated, with its baptistery totally flooded and its historic, mosaic floors covered by 90 cm (2.95 ft) of water.
"The exceptional wave of bad weather leaves us with a dramatic toll: nine dead, four serious injuries and one person missing, " said Interior Minister Matteo Salvini.
Veneto regional governor Luca Zaia says flooding could reach the levels of the 1966 flood that struck both Venice and Florence.
Officials closed major tourist attractions in Rome, including the Colosseum and Roman Forum, early because of heavy rains.