The 40-year-old actor-director was keen to take on the project but has been forced to drop out because of his busy schedule, reported Variety.
A new actor will be sought to star opposite Stewart, with the the movie still tipped to begin shooting in spring 2013.
"Focus" will be written and directed by Glenn Ficarra and John Requa (Crazy, Stupid, Love) and features an experienced con artist showing a newcomer the tricks of the trade.
Affleck is planning to direct an adaptation of Stephen King horror novel 'The Stand', and is also preparing to write, direct and star in a big-screen version of Dennis Lehane's 'Live By Night'.
