In a blog post entitled, "Conscious Uncoupling", the pair say in a joint statement: "It is with hearts full of sadness that we have decided to separate.
"We have been working hard for well over a year, some of it together, some of it separated, to see what might have been possible between us, and we have come to the conclusion that while we love each other very much we will remain separate."
It went on: "We are, however, and always will be a family, and in many ways we are closer than we have ever been. We are parents first and foremost, to two incredibly wonderful children and we ask for their and our space and privacy to be respected at this difficult time.
"We have always conducted our relationship privately, and we hope that as we consciously uncouple and coparent, we will be able to continue in the same manner."
The pair have notoriously spent the majority of their decade-long marriage avoiding being photographed together, with only a handful of snaps being taken since 2003.
As news of the split broke, they were reportedly on holiday together in the Bahamas with their two children - daughter Apple, aged nine, and seven-year-old son, Moses.
Gwyneth has previously spoken about how hard marriage can be, admitting that the couple have gone through "terrible times".
"It's hard being married," Gwyneth said to Glamour magazine. "You go through great times, you go through terrible times. We're the same as any couple.
Gwyneth and Chris at Sean Penn's Help for Haiti Gala in 2014
"I asked my dad once, 'How did you and mum stay married for 33 years?' And he said, 'Well, we never wanted to get divorced at the same time'. And I think that's what happens.
"When two people throw in the towel at the same time, then you break up. But if one person's saying, 'Come on, we can do this', you carry on."