The 24-year-old played the full 2-2 Premier League draw with Hull City on Saturday, scoring one goal and setting up another. However, he reportedly picked up the knee problem after an awkward landing during an aerial challenge.
The Brazilian Football Confederation (CBF) confirmed Pedro's withdrawal but has not revealed the severity of the injury or how long he is expected to be sidelined.
Fluminense midfielder Matheus Martinelli has been called up as his replacement.
Pedro's injury will also be a concern for Chelsea as they prepare for their next Premier League match against Brentford on Friday at the Gtech Community Stadium.
Chelsea will then face the possibility of being without their in-form forward when Brazil begin their international schedule. Brazil are due to play Australia on September 25 and September 29 before meeting India in Kolkata on October 3.
Chelsea and the CBF are yet to provide a detailed recovery timeline for Pedro.
Chelsea manager Xabi Alonso has given his players every chance of returning for Friday's Premier League meeting with Brentford, with Joao Pedro, Reece James and Moises Caicedo all still in contention.
Romeo Lavia believes he is finally benefiting from the work he has put into overcoming his injury problems as he looks to establish himself at Chelsea.
Elliot Anderson has revealed how facing Manchester City as a youngster left him dreaming of one day playing for the club.
Tottenham Hotspur have received a welcome injury boost with Pedro Porro set to return for Saturday's Premier League meeting with Aston Villa.
