Part of the funds raised from the auction at Sotheby's will go to Catholic charity Aid to the Church in Need (ACN )to help with its work rebuilding Christian settlements on the Nineveh Plains destroyed by Islamic State (IS).
The project helps displaced Christians, who have been dependent on emergency aid since 2014, to go back to their original towns and villages.
Alfredo Mantovano and Alessandro Monteduro, president and director of ACN (Italy), said in a statement: "We have thanked the Holy Father and assured him that we will use his gift well - by bringing thousands more Christians back to Nineveh."
The sleek, white car with yellow-gold markings was delivered to the Vatican on Wednesday morning.
ACN has thanked the sports-car maker Lamborghini.
The president and director of ACN (Italy) stated: "The gift to the Pope by the car manufacturer is a good example of how big companies can actually help Christians who suffer."
The funds will also benefit two other charities; one helps migrant women who are victims of modern day slavery and prostitution, and the other helps those stricken by poverty in Africa.
