Defender Calum Angus' (30th minute) calm finish at the half-hour mark handed Pune FC a third consecutive win at home.
With this win, Pune FC go joint top of the table with 13 points from five games. The hosts are equal on points with Salgaocar FC and Bengaluru FC and are second behind the Goans on goal difference having played a game less.
After soaking pressure in the early exchanges, Pune FC created the first close chance of the game in the 18th minute. Playmaker Douhou Pierre's cross in from the right fell for Othallo Tabia on the left inside the box only for the defender to shoot into the side-netting with acres of space.
Six minutes later, the hosts survived a close moment. Striker Edmar Fugueira missed a sitter as he kicked Thomas Saikhom's freekick from the right over the bar from three-yards out.
The hosts went close once again in the closing minutes of the first half. Douhou chipped in a ball for Arata Izumi on the right and the India-international sent in a low ball into the box for striker Thongkhosiem Haokip who failed to connect in front of the goal.