Leigh, 48, whose real name is Jennifer Morrow, filed for divorce on Nov. 15 in Los Angeles Superior Court, citing irreconcilable differences.
She's seeking spousal support as well as primary custody of their son, Rohmer, with visitation for Baumbach.
The couple met while Leigh was starring on Broadway as Catherine in Proof, a role she took on in 2001.
"I expect to be with [Leigh] for the rest of my life," Baumbach told PEOPLE at the premiere for his film The Squid and the Whale, just days after they were married in 2005.
The pair most recently co-wrote the 2010 film Greenberg starring Ben Stiller.