The painting has been transferred to the permanent collection of the Palazzo Barberini – the historic home of the family of the portrait’s subject in Rome – where it was first exhibited.
It will be displayed alongside other works by the artist.
Painted in about 1598, it shows Barberini as a bearded cleric apparently issuing instructions with his right hand outstretched.
Barberini was elected to the papacy in 1623 and served until his death in 1644. He was known as a prominent patron of the arts.
Culture Minister Alessandro Giuli said in a statement that the acquisition was “part of a broader project to strengthen the national cultural heritage that the Ministry of Culture will continue to pursue in the coming months, with the aim of making some art history masterpieces accessible to scholars and enthusiasts that would otherwise be destined for the private market”.
“I would like to thank all the institutions, officials, and technicians who have worked with great skill and dedication to achieve such an important result,” he added.
Caravaggio, whose real name was Michelangelo Merisi, died in 1610 at the age of 38.
He was renowned for his chiaroscuro technique, the dramatic use of light and shadow to bring deep psychological realism to the violent scenes that he generally depicted.