Officials gave a range of reasons for the delays, including a huge reduction in the number of voting stations which were cut by 30,000 in a controversial cost-cutting measure.
In Rome, police reinforcements had to be sent in to keep increasingly unruly crowds at polling stations in check.
Police in Naples reported three assaults at polling stations, while voters in Naples threw ballot boxes on the floor in frustration, reported the Ansa news agency.
Some people tried to rush the gates at one station after waiting until nearly midnight. Others simply gave up and went home after hours of waiting in line.
"Here is my ID card; I'm tearing up my ballot because of the terrible organisation," said Franco De Pascale, who finally gave up trying to vote in Naples after two hours.
Controversial closures
Five people, most of them elderly, fainted in the heat of the crowds at a Milan polling station, while an 88-year-old man with a history of heart trouble collapsed and died while he waited in Grosseto, Ansa reported.
Officials gave a range of reasons for the delays, including a huge reduction in the number of voting stations which were cut by 30,000 in a controversial cost-cutting measure.
Politicians also blamed a high turnout, a long and complicated voting form, and the additional mayoral contests taking place in many cities.
"It could be due to the heated climate," said Rosa Russo Jervolino, the centre-left mayoral candidate in Naples, which saw some of the most chaotic scenes.
Polling in Naples finally ended at 0130, but in Reggio Calabria, stations remained open after 0400 - more than six hours after they were scheduled to have closed.
Restrictions lifted
Agriculture Minister Alfonso Pecoraro Scanio, who himself waited for two hours, called for new booths to be brought out to try to ease the congestion.
Officials in Naples eased restrictions and allowed voters to fill out their ballots while they waited.
But not everyone had to wait.
"I'm 105 years old ... let me vote!" cried Maria Mara, before being allowed to the front of the line to the accompaniment of a round of applause from voters in the eastern province of Frosinone.