The company announced in March that a second instalment of the Marvel superhero film was in the works following its record-breaking $200 million opening at the US box office. The film has since grossed over $1.46 billion.
Whedon will also create a Marvel-related TV series for ABC, Disney also revealed.
The Avengers featured an all-star cast including Robert Downey Jr, Mark Ruffalo, Scarlett Johansson, Chris Evans and Jeremy Renner.
Johansson will reportedly earn $20 million to reprise her role as Black Widow in the upcoming sequel.
Renner, meanwhile, has said that he is unsure if Hawkeye will be in another Marvel movie.
Watch the Avengers trailer below:
Picture gallery - Avengers from comic book to screen: