In a further blow to the tourists, skipper Sourav Ganguly was suffering from mild fever and missed the team's training on Monday ahead of the day-night international at the Pindi stadium.
Vice-captain Rahul Dravid said that Ganguly will be assessed by the medical staff on Tuesday morning before a decision to play him is taken.
"What is certain is that Nehra will not be playing," Dravid said. "The left ankle which bothered him on the Australian tour has flared up again. Hopefully he will be fit for the third match."
Nehra held his nerve amid mounting tension to concede just three runs in the last over when Pakistan needed nine, enabling India to win the high-scoring first match at Karachi on Saturday.
Dravid said young left-arm seamer Irfan Pathan may replace Nehra, although the team management has not ruled out blooding rookie Ramesh Powar, an off-spinner and hard-hitting lower order batsman from Mumbai.
The good news for the tourists was that in-form batsman Venkatsai Laxman was fit to play after missing the Karachi match due to a knee injury.
Laxman, who hit three One-day centuries on the recent tour of Australia, is expected to replace Hemang Badani.
Dravid defended the inexperienced bowling attack which proved to be the weak link in the first match -- barring Nehra's last-over heroics.
"It is obviously an area of concern and we are working on it," Dravid said.
"Not many of our guys have played a lot of One-dayers before, so this series is a learning process for them.
"I don't think there is extra pressure on the batsmen to deliver everytime. If the batsmen don't get 350, hopefully the bowlers will bail us out."
India piled up a mammoth 349 for seven in Karachi, but Pakistan responded bravely through a century from captain Inzamam-ul Haq to reply with 344 for eight.
India will play five One-dayers and three Test matches on their first full tour of Pakistan since 1989.