The Transformers star, 29, cited 'irreconcilable differences' in court papers, reports TMZ.
A Los Angeles court spokesperson has confirmed the news.
The date of separation is listed as 15 June and Megan is said to have asked for joint physical and legal custody of the couple's two sons.
A source tells the publication that the divorce is 'very amicable', and that the couple continue to live in the same house.
Reports first surfaced about the pair's marriage earlier this week, when an unconfirmed report in the new issue of US magazine Us Weekly claimed the low-key pair quietly agreed to separate earlier this year.
Megan and Brian have been together for 11 years after meeting on the set of TV show Hope & Faith.
They first became engaged in 2006, but called off their engagement three years later, before getting engaged again in 2010 and marrying a few days later at a small ceremony in Hawaii.
They have two children together: sons Noah, two, and Bodhi, 18 months.
Desperate Housewives actor Brian, 42, is also dad to 13-year-old son Kassius from a previous relationship.
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