The newly-weds, who enjoyed a lavish nuptials in front of celebrity guests on Saturday, travelled by boat to the city hall where they were officially married by former mayor of Rome, Walter Veltroni, who also officiated Saturday's service, reported Us magazine.
Clooney, 53, wore a charcoal grey outfit while the British lawyer wore a white trouser suit and sunhat.
They left the venue 10 minutes later and were whisked away in a water taxi.
The civil ceremony marked the end of the four-day wedding celebrations that began in Venice on Friday.
Earlier in the day the couple were seen exiting their luxury hotel and making their way to a water taxi to attend a brunch with friends.
Talking as he emerged from the Palazzo with his new wife, Clooney said he felt "very good".