Vice-captain Rahul Dravid will take over from Ganguly for the opening Test of the three-match series, an occasion made even more special as it is Pakistan's 300th match.
Ganguly, who injured his lower back during the final One-dayer at Lahore last Sunday, is expected to be fit for the remaining two Tests at Lahore and Rawalpindi.
"It's a horrible feeling to sit out of what will be India's first Test match in Pakistan since 1989," Ganguly said.
"But it can't be helped. The MRI (magnetic resonance imaging) scans did not indicate any serious damage, but the back pain has not reduced."
It will be the second time this season that Dravid will be leading India in a Test match. Ganguly also missed the second Test at home against New Zealand in October following a boil-induced surgery.
Left-handed batsman Yuvraj Singh will take Ganguly's slot as the sixth specialist batsman behind Aakash Chopra, Virender Sehwag, Dravid, Sachin Tendulkar and Venkatsai Laxman.
Tendulkar, who made his Test debut during the previous series in Pakistan in 1989, is the only player from either side to have experienced an India-Pakistan Test match on Pakistani soil.
India have been bolstered by the return of frontline bowlers, seamer Ajit Agarkar and leg-spinner Anil Kumble, who missed the preceding One-day series due to injuries.
Neither has played a first-class match since January 6, when the fourth and final Test against Australia ended in Sydney, but both are in reckoning to make the final 11 for Sunday.
India named 13 for the match, excluding Ganguly and all-rounder Ramesh Powar, to keep their options open about playing two spinners or three seamers on a wicket bereft of grass.
"I am told this is a good Test wicket that will have something in it for the seamers on the first day before it settles down," Dravid said.
Pakistan, looking to make amends for their 2-3 defeat in the One-dayers, played safe by not making a short-list. They will name their team after another close look at the wicket on Sunday morning.
"It is very important to win the first Test to build the momentum for the remaining games," said Multan-born Pakistan captain Inzamam-ul-Haq.
"Test cricket is a different ball game from the One-dayers and we are confident we can beat the Indians. I think Pakistan must take advantage of the fact that India is without its regular captain."
India (from): Rahul Dravid (capt), Virender Sehwag, Aakash Chopra, Sachin Tendulkar, Venkatsai Laxman, Yuvraj Singh, Parthiv Patel, Zaheer Khan, Irfan Pathan, Laxmipathy Balaji, Ajit Agarkar, Anil Kumble, Murali Kartik.
Pakistan (from): Inzamam-ul-Haq (capt), Yousuf Youhana, Imran Farhat, Taufiq Umer, Yasir Hameed, Misbah-ul-Haq, Asim Kamal, Shoaib Malik, Abdul Razzaq, Moin Khan, Shoaib Akhtar, Mohammad Sami, Shabbir Ahmed, Umar Gul, Danish Kaneria, Saqlain Mushtaq.
Umpires: David Shepherd (ENG), Simon Taufel (AUS)
TV umpire: Asad Rauf (PAK)
Match referee: Ranjan Madugalle (SRI)