The superhero blockbuster, based on a character created in 1941 by Jack Kirby and Joe Simon, focuses on a weak man called Steve Rogers who is injected with an experimental serum which transforms him into a muscular superhero.
Captain America, to be released in 2011, will be set during World War II and lead into Marvel's modern-day ensemble movie The Avengers.
Johnston has been in talks to direct the movie for two years, and producer Kevin Feige told The Hollywood Reporter that his history of working on high-profile popcorn films made him the ideal choice for Captain America.
"This is a guy who designed the vehicles for Star Wars, who storyboarded the convoy action sequence for Raiders Of The Lost Ark," he said. "From Rocketeer to October Sky to The Wolfman, you can look at pieces of his movies and see how they lead to this one."