The Argentinian was awarded the money after a successful legal battle against La Razón. A court in Barcelona judged that a columnist in the newspaper had libelled the footballer in an article from 2014 that accused him of doping.
The ruling deemed the author and the director of the paper to be responsible and ordered them to pay the striker €72,783.20.
On Friday, Messi's representatives confirmed that he had donated the money to the charity, and insisted that he will "continue defending himself against insulting or false statements and accusations that attack his honour".
Doctors Without Borders delivers emergency medical aid to people affected by conflict, epidemics, disasters or exclusion from health care.