Zaheer had an arthroscopic labral repair carried out on his left shoulder in South Africa last month, the BCCI said in a statement.
"Zaheer is undergoing rehabilitation in South Africa and is recovering very well. He is expected to return to international cricket by the end of this year," the statement said.
The 30-year-old left-arm bowler suffered the injury while fielding during the Indian Premier League (IPL) earlier this year, although he still played in the Twenty20 World Cup in England in June.
He subsequently missed India's four-match one-day series in West Indies.
India's next assignment is a triangular one-day series involving hosts Sri Lanka and New Zealand from Sept. 8-14, followed by the Champions Trophy in South Africa from Sept. 22-Oct. 5.
