The 24-year-old played the full game for Chelsea in a 2-2 draw with Hull City in the Premier League on Saturday, scoring one goal and setting up another.
Brazil did not specify the nature of Joao Pedro's injury but said in a social media post that Fluminense midfielder Matheus Martinelli had been called up as his replacement.
Brazil will visit Australia for two friendlies on September 25 and September 29, before playing India in Kolkata on October 3.