The Miranda actor and Tamzin, who starred in EastEnders and Red Cap, say they will remain friends and "continue to support each other" when it comes to their two children.
A rep said: "Tamzin Outhwaite and Tom Ellis are sad to confirm they have separated.
"They continue to support each other as parents and will remain friends. They ask for sensitivity at this difficult time."
Tom, 34, and 42-year-old Tamzin were introduced to each other through actor James McAvoy, a mutual friend of theirs, back in 2005.
They married a year later and welcomed their first child, a daughter called Florence Elsie, into the world in 2008. Last year, Tamzin gave birth to their second daughter, Marnie Mae.
Tom currently stars as Gary Preston in Miranda, while Tamzin is due to hit our screens as DCI Sacha Millard in BBC1 drama New Tricks.