He was accompanied by his wife to the airport from where he boarded a Sahara Airlines flight to Delhi and then boarded a connecting Air Deccan flight to Gwalior.
It was learnt he would return to Kolkata after the tie and again join the team before the next match.
Initially Ganguly, being overlooked for the first test against England, informed the CAB that he would only join the team for the March 6 tie against central Zone in the ongoing Deodhar Trophy.
But late last night in a written communiqu to the Board Ganguly said he would join the team tomorrow for the second match.
The change of heart took place over the weekend. First it was Sunil Gavaskar and then Chief Minister Buddhadeb Bhattacharjee who advised him against quitting.
''I am sad. Anyone will be sad if left out of the squad. I am no different'', Ganguly said after being exluded.
During the weekend he has also reportedly talked to a senior office bearer of the BCCI, who has advised him to continue, as fortunes may change no matter what the chairman of the National selectors felt, with a couple of bad innings or an injury.
Meanwhile, East Zone are in deep trouble after the batting blues against South. They play West Zone tomorrow that feature among others players like Munaf Patel, fresh from destroying England.