The fresco, long believed to have been lost, is attributed to master painter Pietro Cavallini (1250-1340) of the Roman school.
It predates the frescoes at the Basilica of St Francis of Assisi by the Florentine painter Giotto, who is considered to be the father of Western art.
Giotto (1266-1337) is credited with departing from the stylised art form of his time towards a more rounded style, to show details of facial expression and emotion.
'Neglected genius'
But the discovery of the lost Cavallini fresco in the Church of Santa Maria in Ara Coeli could force art historians to rethink their thesis.
"Hidden by a painting by a disciple of Caravaggio, the very well-preserved and complete fresco could be attributed to a master from the late 1290s, a little before the cycle of Assisi," said Tommasso Strinati, an art historian from the University of Rome who discovered the painting.
Cavallini is best known for his large-scale fresco on the life of the Virgin Mary, at Trastevere in Rome, dated 1291.
Often called the "neglected genius", most of his masterpieces have disappeared - some said to have been destroyed during the rebuilding of the Ara Coeli church in the 16th century.
Discovery
Mr Strinati, an expert in medieval art, said he began searching the side chapels and transepts at Ara Coeli at the beginning of the year, in the hope of uncovering some of the lost work.
"To my astonishment the frescoes began to appear when we removed some undistinguished overpainting in one of the side chapels," he is quoted as saying in The Times of London.
"First the head of St Peter emerged, then an angel and then the great figure of Christ," he said.
Another fresco, not yet fully uncovered, depicts a red tower with cherubs - the tower is said to be very similar to one among the Assisi frescoes.
In 1997, the late Frederico Zico, widely regarded as Italy's leading art expert, suggested that several of the frescoes at Assisi were not by Giotto at all.
Instead, he argued, they were "clearly by the same hand" as the Trastevere frescoes - Cavallini.