The Pope made the historic remarks in a new documentary film, "Francesco," which was released in Rome on Wednesday.
"Homosexual people have a right to be in a family. They're children of God and have a right to a family. Nobody should be thrown out or be made miserable over it," the Pope said in the film, the Catholic News Agency reported.
"What we have to create is a civil union law. That way they are legally covered," the Pope said.
Francis has suggested in past interviews that he is not against civil unions, but this is the first time as Pope that he has directly come out in favor of them.
As Archbishop of Buenos Aires, Francis advocated for same-sex civil unions as an alternative when Argentina was discussing whether to legalize same-sex marriage.