As a row erupted over the efficacy of the measures, Milan and the nearby town of Pavia banned cars from their roads between 10:00am and 4:00pm for three days starting on Monday.
In Rome, owners of cars with odd-numbered plates were ordered to leave them at home for the day. On Tuesday, cars with even-numbered plates will be targeted under a measure used three times this month with limited effect.
Traffic restrictions were also in place in the southern city of Naples, where only vehicles operating to an emissions standard known as Euro 4 are allowed to circulate this week.
With many Italians on holiday between Christmas and New Year, the measures were seen as largely symbolic and the authorities have been attacked for backing them up with only limited enforcement measures.
Air pollution contributed to 84,400 premature deaths in Italy in 2012, according to the latest report for the European Environment Agency. Of these 59,500 were attributed to elevated levels of fine dust particles in the air, the problem which has caused this week's alerts.
"This morning, the streets were deserted but it's not only because of the driving ban. Am I the only person working this Monday?" one Milan resident wrote on Twitter.
After several weeks with little or no rain in much of Italy and weather balmy enough to have sent many Romans to the beach for their Christmas lunches, pollution levels measured by the number of fine dust particles in the air have shot up.
Numerous locations have exceeded the 50 mg per cubic metre level which the World Health Organization regards as a ceiling which should not be exceeded in the interests of the general wellbeing of urban populations.
A figure of 102mg/m3 was registered in Milan, which breached the WHO threshold for the 32nd day in a row and its 97th since the start of 2015.
The traffic ban "is a response to an exceptional emergency," the city's mayor Giuliano Pisapia said. "The measure does not bring the city to a standstill but it does have a strong deterrent effect."
Milan is seeking to address its pollution problem by expanding car sharing, a municipal bicycle scheme and its underground rail network, with work now under way on a fifth line in a city which, with its suburbs included, is home to more than eight million people.
Environment Minister Gian Luca Galletti has called an emergency meeting of regional and municipal leaders for Wednesday to discuss coordinating anti-pollution measures.
The alternate days car ban in Rome is aimed at cutting traffic volume by only 20 percent and research has suggested even this limited target is rarely achieved. The mayor's office vowed Monday to step up enforcement with 150 police patrols delegated to check for drivers ignoring the ban.
Consumer group Codacons said the key to beating pollution was providing residents with alternatives to the car.
"If Rome had an artery system (of public transport) comparable to other European capitals, the number of cars in circulation would automatically be reduced all year round," it said.
Rome has only two metro lines and potential expansion of the underground network is limited by the archaeological riches buried beneath the city. In recent years the capital has been repeatedly gripped by financial crises which have led to cutbacks on bus services.
Relief from the smog is at hand but not from any government measure: cool winds forecast for the end of the week are expected to cut the volume of particles in the air.