Deschanel, who married the Death Cab for Cutie singer in September 2009, filed for divorce in October 2011.
According to court papers, the couple's divorce proceedings were finalised in a Los Angeles Superior Court on December 12, reported People magazine.
The court filings read, "Unhappy and irreconcilable differences have arisen between the parties, which have caused the irremediable breakdown of their marriage. There is no possibility that counselling ... Or mediation could save the marriage."
When asked in 2011 about her divorce proceedings, Deschanel had said, "We're friendly. It's all fine."
Since her split from Gibbard, the actress has been linked to her "500 Days of Summer" co-star Joseph Gordon-Levitt, rumours that both actors have adamantly denied.