"What we found today confirms the precise corroboration between the historical documents and the preliminary results that emerged from geo-radar soundings," said Stefania Romano, a spokeswoman for the group behind the excavation at the former convent of Saint Orsula.
The team of historians plan to use geo-radar equipment to locate the skull of Lisa Gherardini Del Giocondo, who died in Florence in 1542 and is believed to have modeled for Leonardo's celebrated portrait, now hanging in the Louvre.
Once they locate the skull, the team will try and recreate a likeness of what the woman would have looked like, compare her to Leonardo's world-famous portrait and unlock the centuries-old mystery surrounding the Mona Lisa's identity.
The historians will compare the DNA with that of two her children buried in Florence's Santissima Annunziata church to prove her identity, although some experts says Leonardo's final portrait may be a composite of other faces.
The Mona Lisa has exceptionally large hands and some art historians believe the sitter was a man - Gian Giacomo Caprotti, apprentice to and alleged lover of the maestro. Many have wondered if a secret lies behind the model's famously cryptic smile.
But most modern scholars now agree the Mona Lisa sitter was Del Giocondo, the wife of a rich Florentine silk merchant who according to Leonardo sleuth Giuseppe Pallanti became a nun after her husband's death and died in the convent on July 15, 1542, aged 63.
The dig began on Wednesday in the hallways of the convent and Roman said the team's radar had shown there could be burials there dating back to Gherardini's time as little as two metres below the surface of what was formerly a cloister.
"In the next few days we will enter the most critical phase of the research, when the tombs are opened and we find if there are human remains inside or not," said Romano.
If found, Mona Lisa's body will be examined by archaeologists, art historians, anatomic pathologists, anthropologists and biologists, and the tomb and investigation finding with go on public display, according to Romano.
The excavation has sparked controversy, however, with a local princess who claims to be related to Del Giocondo calling it "sacrilegious" and saying the remains should be left in peace.