Imposing the limit, which might later be modified, will "allow everyone to better enjoy the fountain, without crowds or confusion", Roberto Gualtieri told journalists in front of the famous landmark.
Gualtieri also said the city authorities were considering charging a modest entry price to finance, among other things, the fountain's upkeep.
The clean-up of the fountain and other key city sites, is aimed at "returning most of the monuments to the city in time for the start of the Jubilee" Claudio Parisi Presicce, Rome's superintendent for cultural heritage sites, told AFP-TV.
The jubilee of the Catholic Church begins on December 24.
The Trevi fountain, a baroque masterpiece, is one of the most visited sites in Rome.
Featured in many films set in the city, it famously appears in a classic scene in Federico Fellini's "La Dolce Vita", when Anita Ekberg invites Marcello Mastroianni to join her in the fountain's basin.
Sunday's reopening took place under light rain in the presence of several hundred tourists, many of whom followed the mayor by throwing a coin into the fountain.
Between 10,000 and 12,000 tourists a day used to visit the Trevi Fountain.
Making a wish and tossing a coin into the water is such a tradition that the city authorities used to collect around 10,000 euros ($10,500) a week. That was turned over to the Caritas charity to provide meals for the poor.
The three-months cleaning project involved removing mould and calcium incrustations.
The Trevi fountain is just one of the sites being cleaned up across the Italian capital as it prepares for the arrival of the 33 million people expected in 2025 for the Jubilee.
This event, declared by Pope Francis, is a year of pilgrimage and prayer, marked by religious and cultural events held across the Vatican and Rome. It takes place roughly every 25 years.
