The Tomb Raider actor told America's Inside Edition that he learned of the divorce proceedings via Angelina's brother James Haven, rather than the actress herself.
He said: "It's very sad. Something very serious must have happened for Angie to make a decision like this... I am concerned for Angie and the children and hopefully I will be seeing them very soon."
Jon said he wasn't aware of the reasons behind the split.
He has had a famously rocky relationship with Angelina in the past. They spent many years estranged from each other, after Jon commented on Angie's mental health in an interview. But they mended their relationship around six years ago, when Angelina began to expand her family.
Oscar-winning actress and humanitarian Angelina, 41, shocked the showbiz world on Tuesday (20 September) when she announced via her lawyer that she'd filed for divorce from Brad, 52, after two years of marriage. They had been together for 12 years and share six young children.
Angelina's attorney said on her behalf: "This decision was made for the health of the family. She will not be commenting at this time, and asks that the family be given their privacy during this difficult time."
Brad later responded with his own brief statement, simply saying: "I am very saddened by this, but what matters most now is the well-being of our kids."
They share children Maddox, 15, Pax, 12, Zahara, 11, Shiloh, 10, and twins Vivienne and Knox, eight.
According to legal papers cited in the US, Angelina has requested full sole custody of the children, with Brad having visitation rights. Neither star's rep has commented on the legal documents.
This is Angelina's third divorce following marriages to actors Johnny Lee Miller and Billy Bob Thornton, while Brad was famously wed to Jennifer Aniston.
Brad was still married to Jen when he met Angelina while filming the action comedy Mr and Mrs Smith about a married couple who don't realise each has a secret career as an assassin. There has always been speculation that Brangelina fell for each other on set, which seemed to be confirmed when Brad once commented their children could watch the movie where their parents fell in love.