Lee Ho-Jin, 56, who lost his youngest son in the tragedy, was baptised in a simple ceremony at the Vatican embassy in Seoul, choosing Francis as his baptismal name.
Lee had asked the pope to baptise him when Francis held a private audience with a group of Sewol survivors and victims' relatives before holding a mass in the central city of Daejeon on Friday.
"The pope was only too happy to be able to conduct an unscheduled baptism of an adult into the Korean Church," spokesman Federico Lombardi said.
The Sewol ferry capsized on April 16 off the southern coast, with the loss of 300 lives, most of them high school students on an organised trip.