The couple wed in 2005.
Leigh, 48, and Baumbach, 41, had worked together on "Margot at the Wedding"(2007) and "Greenberg" (2010), which Leigh also co-wrote.
In a Los Angeles Superior Court filing, Leigh cited irreconcilable differences as the reason for the break up.
The couple's infant son was born seven months ago. Leigh is seeking physical custody of the child.
Leigh is best known for her roles in "Single White Female," "Fast Times at Ridgemont High," and "Georgia."
Baumbach scored his biggest success with "The Squid and the Whale," which drew on memories of his parents' breakup.
Pamela Chelin contributed to this report.