"As a precaution we opted to clear tourists from [St Mark's] Square", Venice Mayor Luigi Brugnaro said in a video from the flooded scene that was posted on his Twitter account.
Venice has been devastated by the worst floods to hit the lagoon city in at least a decade, as heavy rain and high winds sweep across Italy.
Two people were killed in Terracina 100 kilometers (62 miles) southeast of Rome after a tornado swept through the town and caused a tree to fall on their vehicle, according to state broadcaster RAI.
High winds toppled trees that killed passers-by in four incidents in Naples, Lazio and Liguria.
In the northern canal-ringed city of Venice, local authorities said the "acqua alta" (high water) peaked at 156 centimeters (61 inches). The high tide along the final stretch of the race meant participants had to jog through ankle-deep water to complete the course. The highest ever recorded was 194 centimeters in November 1966.
Tourists and residents trudged through the waist-high water, while shops and restaurants were inundated as barriers placed across doorways failed to hold back the rising tide.
Three quarters of the city of Venice is under water as gale-force winds and torrential rain brings chaos to Italy. Shopkeepers used buckets to remove water from their premises. In 2003, Italy began construction on a massive system of surge protection gates around Venice, but fifteen years and €5.5 billion euros later the project is still unfinished.
Much of the country is under alert for flooding and the Interior Ministry urged officials in the affected regions to consider closing schools and offices again on Tuesday.
The fatalities 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 windsurfing in Emilia-Romagna. Further south, the ancient Roman city of Pompeii was shuttered because of the blustery conditions.
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