In a statement released to People, Jane said: "Lara and I have decided to end our marriage. This has been a difficult decision for us as we care very deeply about one another. We ask for privacy as we deal with this family matter."
Jane, 52, and Lara, 44, first in 2009 at a fundraiser in San Francisco at which Embry was receiving an honour.
The pair got engaged in 2010 and got married on Memorial Day the same year in an intimate ceremony in Sunderland, Massachusetts - which is one of only a handful of US states where gay marriage is recognised.
Lara has got a daughter called Haden who Jane got very close to during the relationship, previously describing her as her "greatest pleasure" in life.
Jane - who plays tough cheerleader coach Sue Sylvester in the musical drama - previously said: "My greatest pleasure is Haden, my stepdaughter.
"I am surprised how much love you feel and how you would do anything for your children.
"Some may say I know a thing or two about playing intimidating authority figures but she knows how important love and acceptance is.
"I am in love and in awe with Haden. I like watching her walk through the world without fear. She happens to be an exceptional human being and one of the most fair, open-hearted, embracing people I have ever met - grown-up or child."