Striker Lalpekhlua (5th minute) and winger Katsumi (76th) handed Pune FC their fifth loss of the season and the third at home.
Having dropped points, Pune FC (23 pts) stayed in the fifth place while Mohun Bagan (31 pts) increased their lead at the top.
With this game, Pune FC ended their home campaign in the league with four wins, three draws and three losses.
Going into the game, Pune FC Coach Karim Bencherifa made four changes handing starts to Srikanth Ramu, Darko Nikac, Edgar Marcelino and Dhanpal Ganesh.
More From This Section
Having conceded early for the second game in a row, Pune FC began to press up from the flanks but were falling short in the final third. Meanwhile, at the other end, Jeje once again went close after getting into the clear on the left but his grounder drifted wide.
As the half progressed, Pune FC began to see more of the ball but were finding it hard to penetrate into the box. Defender Munmun Lugun sent in a couple of crosses from left but the Bagan backline managed to clear.
Pune FC made the first change in the final five minutes of the half as Coach Bencherifa brought in striker Prakash Thorat in place of Ganesh to add more firepower up front.