The appointment comes five weeks after Prodi won a narrow victory over Berlusconi. Prodi pledged for form a "solid" government, ANSA reported.
At a farewell news conference, Berlusconi said the election results would be re-examined.
"There are lots of irregularities," he charged. Prodi's victory was the narrowest in Italian post-war history, ANSA said.
Prodi has put together a nine-party coalition, which critics say is too disparate to govern. The alliance includes communists, anti-clerics and staunch Roman Catholics, ANSA said.
Prodi, 66, was first appointed prime minister in 1996 but his government failed in 1998 amid intra-coalition squabbling.