Zaheer managed just three overs in Saturday's tour match against Northants,.
India's pace bowler Zaheer Khan will miss the rest of the England tour with ankle and hamstring injuries.
A statement from the Indian cricket board said: "He will need at least 14-16 weeks to recover completely."
RP Singh has been called up but faces a race to be ready for the third Test, starting at Edgbaston on Wednesday.
India lost spinner Harbhajan Singh and batsman Yuvraj Singh to injuries during the Trent Bridge defeat, which saw them go 2-0 down in the four-Test series.
Zaheer sustained a hamstring injury in the first Test at Lord's after bowling just 13.3 overs, and missed the second match of the series.