Zaheer, suffering from a suspect hamstring injury, will return home on Monday, the day the second Test begins in Lahore.
Team manager Ratnakar Shetty said the decision to send the Baroda paceman home was taken after considering medical opinion.
"After considering the reports of the scan and the opinion of the specialist as well as team physio Andrew Leipus, it has been decided that Zaheer will return home on April 5," he said adding the chances of his recovery before the third Test was in doubt.
Zaheer had already been ruled out of the second Test.
Left-arm paceman Ashish Nehra, who played in the first two One-dayers but missed the first Test due to a split webbing in his bowling hand, has already been flown in as a reinforcement for the bowling attack.
Skipper Sourav Ganguly, nursing a back problem, will also miss the second Test although he is expected to join the team ahead of the third match beginning on April 13. Middle-order batsman Mohammad Kaif has replaced the captain in the squad.