The actor and the pontiff discussed their shared concern over the environment and Leonardo DiCaprio gave him a cheque from his charitable foundation.
Speaking in Italian the Titanic and Wolf of Wall Street actor said: "Your Holiness, thank you for granting me this private audience with you."
Mr DiCaprio also gave Pope Francis a book of works by the 15th-century Dutch painter Hieronymus Bosch and showed him the reproduction of Bosch's Garden Of Earthly Delights that had hung over his cot as a child.
The image shows Adam and Eve in the first panel, a teeming landscape in the centre panel, and finally a vision of hell.
DiCaprio said: "As a child I didn't quite understand what it all meant, but through my child's eyes it represented a planet, the utopia we had been given, the overpopulation, excesses, and the third panel we see a blackened sky that represents so much to me of what's going on in the environment."
He also said the painting showed the pair's concern for the environment.
Pope Francis' encyclical on the environment denounced the world's fossil fuel-based economy and its demand for greener energy sources.
Francis gave DiCaprio a leather-bound copy of Laudato Si and his earlier document, The Joy Of The Gospel.
Di Caprio is nominated for an Oscar for his role in his most recent film The Revenant.