Us Weekly broke the news, which Deschanel's rep confirmed. A source added: "It was mutual and amicable. There was no third party involved."
The actress and singer, 31, and Gibbard, 35, have only been married for two years; they tied the knot near Seattle, Wash. in Sept. 2009.
Their mutual music manager set them up three years ago -- Deschanel is also one-half of indie music duo She & Him, with M. Ward. Since then, Gibbard has talked openly about having an an instant crush on Deschanel: "I was just awestruck that she was even talking to me."
What surprised Deschanel most about married life? In her September cover story in New York magazine, she said: "You can't expect to make no effort. You still have to make the effort and be kind and understanding. It sort of just solidifies your commitment."
Deschanel's 'New Girl' was the first new show of the fall TV season to get a full season pick-up; it airs Tuesdays, 9PM ET on Fox.