Umesh Yadav was named as Bumrah's replacement for the Test series, starting October 2.
"Bumrah has sustained a minor stress fracture in his lower back and has been ruled out of the upcoming series against South Africa," BCCI said in a statement.
''The injury was detected during a routine radiological screening. He will now undergo rehabilitation at NCA and will be monitored by the BCCI Medical Team,'' the statement added.
In the recently concluded 2-match Test series against West Indies, Bumrah was in phenomenal form and had picked 13 wickets at an average of just 9.23.
The injury means Bumrah will have to wait to play his first Test at home. He has been the pace spearhead for India in recent times, picking 62 wickets in 12 Tests, all away from home.
The first Test begins on October 2 in Visakhapatnam before the series moves to Pune and Ranchi.
India squad: Virat Kohli (Capt), Mayank Agarwal, Rohit Sharma, Cheteshwar Pujara, Ajinkya Rahane (vc), Hanuma Vihari, Rishabh Pant (wk),Wriddhiman Saha (wk), R Ashwin, Ravindra Jadeja, Kuldeep Yadav, Mohammed Shami, Umesh Yadav, Ishant Sharma, Shubman Gill.(UNI)
