The day of mourning marks the end of a month in which Italy saw more deaths from a single disaster than at any time since World War II.
Italians lowered their green, white and red national tricolour as well as the flags of their cities and of the European Union, while the Vatican lowered its own yellow-and-white flags.
The initiative was promoted by a group of mayors to show solidarity with the towns suffering the most in the north, the epicentre of the crisis.
Italy is the world’s hardest hit country in terms of deaths and accounts for more than a third of all global fatalities.
“This moment of silence of mayors, in which even the presidential palace and the Vatican participated, is an important moment for our country, showing unity from north to south,” Bari Mayor Antonio Decaro said.
“All the mayors have gathered together in a kind of ideal embrace, most importantly to be close to the places that are suffering the most, where the virus has been the most ferocious, to be close to the mourning for those who have died.”
Mayors wearing their official tricolour sashes and some donning surgical masks looked on sombrely as buglers played on empty streets that before the lockdown to try to contain the virus would have been packed with residents and tourists.
Venice Mayor Luigi Brugnaro stood by the unusually still waters of a canal, free of boat traffic because of the nationwide lockdown.
The lockdown was due to end on Friday, but has been extended until sometime after Easter, which falls on April 12 this year.
Stores and restaurants are not expected to start opening until at least May, and no official is willing to predict when life might return to the way it was just a month ago.
While there is evidence that the pandemic is slowing in Italy, authorites have said this does not mean measures will be lifted and continue to urge people to remain at home.
Prime Minister Giuseppe Conte said any easing of containment measures would be done incrementally to ensure Italy does not undo any progress made against the disease.