The director had been sued for $2 million by producer Amanda White and $2.25 million by cinematographer Magdalena Gorka earlier this year.
They had accused Affleck of acting inappropriately during production of the documentary, which follows Joaquin Phoenix as he attempts to make the switch from movies to music.
In a statement, Affleck's representative said: "The disputes between Flemmy Productions, LLC and Casey Affleck with Amanda White and Magdalena Gorka in connection with the film I'm Still Here have been resolved to the mutual satisfaction of the parties and the lawsuits are being dismissed."
Affleck had previously denied the allegations of both women. The financial details of the settlement have not been revealed, although it is thought White and Gorka will still be credited on the movie.