The Minority Report star had already completed work on her role as the voice of an operating system in forthcoming drama Her, but the filmmaker subsequently decided to take the project in a different direction and hired The Avengers beauty to step in.
In a statement released to Vulture.com, Jonze insists recasting roles as he works is nothing out of the ordinary for him and he has nothing but praise for Morton.
He writes, "I think, unfortunately, it's pretty normal in terms of my not-quite-painless-for-everyone-involved 'process' of discovering what the movie is.
"Samantha was with us on set and was amazing. It was only in post production, when we started editing, that we realised that what the character/movie needed was different from what Samantha and I had created together. So we recast and since then Scarlett has taken over that role."
He adds, "I love Samantha. I've been friends with her forever and I hope we make lots of things together in the future."
Johansson joins Amy Adams and Rooney Mara among the cast of the new movie, about a lonely writer, portrayed by Joaquin Phoenix, who begins to develop feelings for his new operating system.