People.com said Gilbert, 44, filed legal separation documents in Los Angeles on Friday.
UsMagazine.com said the documents cited irreconcilable differences as the cause for Gilbert's breakup with the 54-year-old, former 4 Non Blondes front-woman.
The date of separation was listed as Aug. 13.
The women began dating in 2011 and share a 4 1/2-year-old son, Rhodes Emilio. Gilbert also has a son and daughter from a previous relationship.
Gilbert stepped down from her job as co-host of The Talk in August after nine years.
"I obviously love it here and like I said, this was extremely difficult," she said at the time.
"Last season, I did The Conners, as you know, and was also producing, and here, and I loved it and felt totally empowered, but also if I'm being honest about it, I think my life was slightly out of balance and I wasn't able to spend as much time with my three kids as I'd like, and time for myself," Gilbert said.
"As I've continued on, I'm starting to develop more things to produce and I'm having opportunities to act, and I'm just feeling like I don't know how I'm going to do it. I was looking at the next six months and just thinking, 'There's no time,'" she added.