Sony Pictures Entertainment announced the project, which was first revealed in October 2010 under the name One Thousand AE.
The story takes place 1,000 years in the future and focuses on "a young boy who navigates an abandoned and sometimes scary Earth to save himself and his estranged father after their ship crashes".
Columbia Pictures president Doug Belgrad said in a statement: "Night is an outstanding filmmaker who has a tremendous vision for this science-fiction adventure story and we couldn't be more excited to be working again with Jaden after our experiences on The Pursuit of Happyness and The Karate Kid. We're thrilled to have the two of them together on this project."
"The chance to make a scary, science-fiction film starring Jaden and Will is my dream project," added Shyamalan.
Will Smith's production company Overbrook Entertainment will co-produce the script, which was written by Shyamalan and Gary Whitta.
Will was recently announced to be starring in an upcoming remake of the story of Job, penned by The Fighter writer Paul Tamasy.