Two protestors were injured in the violence as opposition against Turkish president Recep Tayyip Erdogan’s visit mounted.
Italian authorities had ordered a 24-hour ban on protests in the centre of the capital in anticipation of the protests.
Mr Erdogan, who is accused of limiting free speech in Turkey by jailing journalists and opposition Kurdish politicians, was in Rome from Sunday night to early Monday evening.
A pro-Kurdish group held a sit-in outside the Castel Sant’Angelo, an ancient mausoleum near to where Mr Erdogan was meeting Pope Francis at the Vatican.
The demonstrators, who object to the President’s treatment of Kurds in Turkey and Syria, carried signs reading “Erdogan killer” whilst chanting “shame shame”.
They attempted to march towards St Peter’s Square in the Vatican, according to the Italian press agency Ansa.
Baton-wielding police dressed in riot gear stopped protestors, with images showing clashes between officers and the demonstrators.
Two people were arrested, according to Ansa.
The agency reported that one demonstrator shouted: “So much for your democracy.
“Today we’re here to defend our mothers and children.
“You and the Pope lost.”
Mr Erdogan met Pope Francis for just under an hour this morning, where the pontiff handed him a medallion embossed with an angel strangling a “demon of war”.
The image is said to be a symbol of peace and justice.
Pope France and Mr Erdogan discussed the state of Jerusalem and tensions in the Middle East, the Vatican’s press office said.
The two are also said to have discussed the challenges facing Turkey as it takes in huge numbers of refugees.
Mr Erdogan’s Italy visit, the first of its kind in nearly 60 years, was also scheduled to include a meeting with the President Sergio Mattarella and Prime Minister Paolo Gentiloni.
Illegal immigration, defence and EU membership featured on the agenda.
The leader of Italy’s far-right North League, Matteo Salvini, said he was “ashamed that Italy is welcoming the representative of a bloodthirsty extremist regime, from a de facto Islamic country where religion rules over law.”
(Additonal reporting by Maria Ortega.)