Goalkeeper Gianluigi Donnarumma donned knee-high wellington boots along with Italian football federation (FIGC) president Gabriele Gravina to visit the inundated St Mark's Square.
The iconic square had been reopened earlier Saturday after unusually intense "acqua alta", or high water, which hit its highest level in half a century.
"On behalf of the whole team, we stand close to the city of Venice," said AC Milan's Donnarumma.
The FIGC delegation visited several businesses damaged by the flooding, and chatted with Venetians, volunteers and police.
"Venice will overcome this too. Like an athlete who suffers a serious injury and then gets up again," said delegation chief Gianluca Vialli.
"Venice is a wounded city, but it is strong as well as being wonderful, and has shown great character and an extraordinary ability to stand up," said Gravina.
Italy coach Mancini later signed autographs as 200 fans were allowed to watch the team's training session at the city's 'Taliercio' sports centre, which had initially been planned behind closed doors.
The visit also coincides with the unveiling of a partnership agreement between the four-time world champions and Venice Airport, later on Saturday.
The Azzurri will on Sunday travel to Palermo for their final Euro 2020 qualifying game against Armenia.
The Azzurri have bounced back impressively after failing to qualify for last year's World Cup for the first time since 1958.
Italy registered a record 10th straight win as they eased past Bosnia and Herzegovina 3-0 in Zenica on Friday.