What seemed like a clean goal from Bagan's Nigerian striker Odafa Okolie initially was later confirmed that it was an own goal by Air India's Fernandes.
The deflection from Fernandes in the 68th minute led to Air India's third straight loss, but the win for Bagan helped them climb up to the 10th position in the points table.
Both the teams had started their I-League season on a disappointing note and with three points on the table, Bagan can now heave a sigh of relief.
Okolie, who has not been in good form of late, looked to be in a much better shape today. He had three shots on target but Air India goalkeeper Gagandeep Singh was up to his task.
In the second half, Okolie was in full form as he took shots on almost all the balls he got inside the 30-yard line. One of his shots hit the right side of the goal post that saved Air India from further blushes.
Air India's Junior Obagbemiro had a chance of an equaliser, but Bagan goalkeeper Shilton Paul raced from the goal-line and saved the attempt.
Junior took the ball ahead but failed to score as he shot the ball wide.