Alfano met Government of National Accord head Fayez al-Sarraj and his vice president Ahmad Meitig to discuss "efforts being made towards national reconciliation", the GNA said in a statement.
Alfano's trip to Libya came hot on the heels of a two-day visit on Thursday and Friday to the oil-rich North African nation by his British counterpart Boris Johnson.
Johnson met Sarraj on Thursday and congratulated him on meeting earlier this week in Abu Dhabi with Libyan military strongman Khalifa al-Haftar, who does not recognise the GNA's legitimacy.
Italy, too, has welcomed the meeting between Haftar and Serraj. The foreign ministry has said that Alfano's visit was aimed at renewing Italy's support for peace efforts to ensure Libya's stability.
Alfano and Libyan leaders also discussed ways of curbing the influx of migrants trying to reach Europe from Libya, as authorities Saturday said that hundreds of migrants were rescued by the Libyan coastguard.
The Libyan judiciary in March suspended a deal struck the previous month between Libya and Italy aimed at bolstering joint efforts to stop the flow of migrants.
In April, the Italian government said that a dozen of rival tribes in southern Libya had agreed to cooperate on securing the country's borders to prevent illegal migration.
Sarraj has struggled to impose the authority of his fragile government, which continues to meet resistance at home despite its backing by many political and military leaders.
Six years after a revolution that toppled dictator Moamer Kadhafi, Libya has become a key departure point for migrants risking their lives to cross the Mediterranean to Europe.
Each year, thousands of people, mostly from sub-Saharan countries, board boats operated by traffickers in the country's west heading for the Italian island of Lampedusa, some 300 kilometres (190 miles) away.
In the first three months of 2017, more than 24,000 migrants arrived in Italy after making the perilous crossing from Libya, up from 18,000 in the first quarter of last year, according to the UN refugee agency UNHCR.
READ MORE: The changing face of the Mediterranean migrant crisis
Photo: Andreas Solaro/AFP