Ganguly failed a fitness test in the afternoon and was replaced by Hemang Badani.
Rahul Dravid will lead the side.
Ganguly struggled during the test, which was conducted by team physio Andrew Leipus and trainer Gregory King.
The doctors refused Ganguly a pain-killing injection that would have let him play, but could have jeopardised his participation in the upcoming Test series in Australia, starting December 4.
To add to India's misery, Dravid lost the toss and was asked to field first by Australia skipper Ricky Ponting.
India went in with five bowlers -- Zaheer Khan, Ajit Agarkar, Aavishkar Salvi, Murali Kartik and Harbhajan Singh -- and six batsmen, dropping Mohammad Kaif from the playing eleven. The reason behind playing only six batsmen is the good form of the batsmen.
Also missing from the playing eleven is spinner Anil Kumble, who was edged out by Murali Kartik, who was not selected for the tour of Australia.
The average score of teams chasing under lights at the Eden Gardens is 180. Which means the Indians will have to come up with an extraordinary performance to win this final.