Author Francesca Pardi, who identifies as lesbian, says she received the letter that also blessed her relationship, according to The Washington Post.
But the Vatican has stressed this is a courtesy letter and does not signify a change in Catholic teaching.
A spokesperson said: "The blessing of the pope at the end of the letter was directed to the person, not at any possible teachings that are not in line with the doctrine of the church - which hasn't changed a bit as the Holy Father has repeated even recently," said Revd Ciro Benedettini in a statement.
The church considers marriage as the joining of a man and a woman.
"Caro Papa Francesco, la mia famiglia ha due mamme e 4 bambini": il Vaticano risponde http://t.co/jyP0kMz14a
— Francesca Pardi (@Francipardi) August 30, 2015Francesca Pardi, posted on social media that her reply from the Vatican included a papal blessing.
The letter was written by a Vatican official on behalf of the Pope.
It wished her "more fruitful activity in the service of young generations and the spread of genuine human and Christian values."
Her books draw on various social issues, including a series that looks at non-traditional family models, such as gay couples, adoption and single parents.
The Mayor of Venice, Luigi Brugnaro, banned the books from schools after the inclusion of same-sex families in some titles.
One book, "Little Egg" tells the story of an egg that meets lots of different animal families, including gay couples.
Francesca Pardi said she sent a letter and books to the Holy Father following the Family Day rally that brought thousands of people to the streets of Rome in June to protest against same-sex families.
Francesca Pardi is in a same-sex marriage and has four children with her partner.
The Vatican is due to host a Synod next month where church leaders will discuss family issues.
LGBT issues will also be on the agenda during the Pope's visit to the United States later this month.
