The couple became parents to a baby boy named Henry on Wednesday, Deschanel's representative told People.
Deschanel and Hornsby - who married in Los Angeles in September 2010 - confirmed the pregnancy in March this year.
Deschanel recently gave an interview in which she said that she was "in awe of the process" of being pregnant, joking that seeing her belly move reminded her of the film Alien.
She also maintained her vegan diet throughout pregnancy with the support of celebrity dietician Ashley Koff.
Deschanel's pregnancy was written into the Bones storyline for the new season, which begins on November 3 at 9/8c on Fox.
Hornsby's new sitcom How to be a Gentleman premieres on September 29 at 8.30/7.30c on CBS.