A first half strike from Thongkhosiem Haokip (27th minute) proved to be the difference between the two sides in a hard fought encounter on a rainy evening at Shivchhatrapati Sports Complex at Balewadi here.
The win was Pune FC's first in four games and helped them leapfrog Mohun Bagan (14 points) to the top of standings with 15 points.
Going into the game, coach Karim Bencherifa made two changes to the lineup, handing starts to Yumnam Raju and Prakash Thorat.
Ten minutes later, Pune FC once again went close when a corner curled in by Lalrempuia Fanai found Luciano Sabrosa in the box. He headed the ball which reached Dhanpal Ganesh who ended up shooting it wide.
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Pune FC broke the deadlock in the 27th minute through some great combination play. Arata Izumi, who was running down the left flank, released the ball for Prakash. He cut the ball in for Haokip who side-stepped the shot deftly beating Wahingdoh's custodian Nikhil Bernard to score his sixth goal of the campaign and making him the sole leader in the I-League top-scorer's chart.
Wahingdoh continued to press for an equaliser through Jackichand. Amrinder twice, in the opening 10 minutes of the second half, stepped up to deny his brilliant efforts, one of which was at close range.
The game gradually moved into Royal Wahingdoh doing most of the attacking and Pune FC retorting on the counter.
In the 86th minute, a powerful shot by Wahingdoh's Reagan Singh hit the crossbar, while another long ranger by Densill Theobald was also denied by the crossbar.
However, Pune FC kept their calm and defended well in the final minutes of the game to clinch a narrow 1-0 win.