They also barred access to the central St Mark's Square, which was heavily flooded.
Six people died in four separate incidents in Naples, Lazio and Liguria, after gale-force winds brought down trees.
Schools have been closed around the country and the authorities have warned against non-essential travel as the Civil Protection Agency issued multiple weather warnings.
In Venice, flooding caused the water level to hit 156 centimeters (61 inches), a 10-year high, and an evacuation of the city's famous St Mark's Square.
Venice frequently floods when high winds push in water from the lagoon, but Monday's levels were extraordinary, with the peak water level the highest since December 2008, according to local statistics.
Cleanup efforts got underway in Venice on Tuesday after a "perfect storm" of high tides and strong winds left three quarters of the historic city underwater on Monday.
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Falling trees killed two people in their vehicle not far from Rome, a man south of the capital and another in the Naples region, authorities said. Footage from the day shows runners plodding on through the flooded town as the water splashed up against their running shorts. Water levels were forecast Tuesday at 110 centimeters (43.3 inches), flooding 12 percent of the famed lagoon city.
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.
Regional governor Luca Zaia has warned that flooding could reach the levels of the disaster that struck the city in 1966.
"Of course if the Moses project was completed the damages we are seeing now would not have happened", he said, "but the project was not completed because of the high cost".
It was the worst flooding seen in Venice for at least a decade.
Some mountainous areas in the north of the Veneto region has already exceeded 400 mm of rain accumulated since Saturday, and the weather services are predicting heavy rainfall.