It reached a high of 1.54 metres (five feet) just before midday - lower than Tuesday's peak but still dangerous.
"I'm forced to close the square to avoid health risks for citizens... a disaster," Brugnaro said. In the afternoon the square reopened as water levels receded and forecasts anticipated lower levels in coming days.
Churches, shops and homes in the city of canals have been inundated by unusually intense "acqua alta", or high water, which on Tuesday hit their highest level in half a century.
"We've destroyed Venice, we're talking about one billion (euros) in damage and that's just from the other day, not today," Brugnaro said, as far-right leader Matteo Salvini joined the list of politicians to visit the stricken city.
The crisis, driven by bad weather, has prompted the government to release 20 million euros ($22 million) in funds to tackle the devastation.
"It's shocking to see this, having water up to your knees," Mexican tourist Oscar Calzada, 19, told AFP Friday.
"You have to be here to believe it and hopefully it won't happen again, it'll only be once-in-a-lifetime type thing."
Surveying the damage, Culture Minister Dario Franceschini warned the task of repairing the city would be huge. More than 50 churches had suffered damage, he said.