Bumrah, the highest wicket-taker in the recent Test series with Australia which India lost 3-1, had back spasms during the final Test in Sydney last month, which also ruled him out of the current white-ball series with England.
His absence will be a major blow to India, with the 31-year-old widely considered one of the best all-format fast bowlers in the sport.
"Fast bowler Jasprit Bumrah has been ruled out of the 2025 ICC Champions Trophy due to a lower back injury. The men's selection committee has named Harshit Rana as Bumrah's replacement," the Indian cricket board (BCCI) announced on Tuesday.
Rana has played two ODIs, both of which came against England this month, picking up four wickets.
The BCCI added that spinner Varun Chakaravarthy, who took 14 wickets in a five-match T20 series against England in January and February, would replace batter Yashasvi Jaiswal.
India are in Group A in the Champions Trophy and play Bangladesh, defending champions and rivals Pakistan and New Zealand.
INDIA CHAMPIONS TROPHY SQUAD: Rohit Sharma (capt), Shubman Gill (vice capt), Virat Kohli, Shreyas Iyer, KL Rahul, Hardik Pandya, Axar Patel, Washington Sundar, Kuldeep Yadav, Harshit Rana, Mohammed Shami, Arshdeep Singh, Varun Chakaravarthy, Rishabh Pant, Ravindra Jadeja.