The left-hander fell to another discard, Zaheer Khan, both times -- clean bowled in the first innings and leg-before first ball in the second -- during the Duleep Trophy final between East Zone and West Zone in Ahmedabad.
It was hardly the performance the selectors were expecting from Ganguly ahead of next month's three home Tests against Sri Lanka.
Ganguly, dogged by poor form, injury and a public row with coach Greg Chappell, was axed as captain last month and replaced by Rahul Dravid for two one-day series against Sri Lanka and South Africa.
Dravid enhanced his claims for a longer tenure after India crushed the Sri Lankans 6-1. They start as favourites against South Africa in the five-match series which begins on Wednesday.
Ganguly, India's most successful Test captain with 21 wins and 5,066 runs in 84 Tests behind him, was expected to return as skipper or purely as a batsman for the first Test against Sri Lanka in Chennai from December 2.
Chairman of selectors Kiran More was non-committal on Ganguly's future.
"We have not written off Sourav or anyone else," More told AFP. "We are only looking at runs and wickets from the contenders and how they will contribute to the team.
"The message is loud and clear. Attitude and performance are critical."
Ganguly and Chappell were involved in a bitter row in September, with the coach saying in a leaked e-mail to Indian cricket chiefs that the captain was unfit to lead the team.
The Indian board brokered a truce, but an elbow injury which forced Ganguly to miss a trial tournament in Mohali last month cost him both the captaincy and a place in the one-day side.
Ganguly returned to score a century in the first Duleep Trophy match but the two ducks in the final of the same tournament could not have been more ill-timed.
Ganguly contributed just 48 in three home Tests against Pakistan early this year and even a painstaking six-hour century in the first Test against Zimbabwe in September did not satisfy critics.
The Indian team for the first Test against Sri Lanka will be picked after the last one-dayer against South Africa in Mumbai on November 28.