Defender Zohmingliana Ralte's second half double strike (74th & 80th minute) handed Pune FC, who are playing in the AFC Cup for the first time this season, a win over the Group-H winners.
The three points earned took Pune FC's overall tally to six points but they remained fourth and last in the group behind Kitchee (13 points), Nay Pyi Taw (8) and Tampines Rovers (6).
In an equally fought opening quarter, it was Jorge Tarres who first went close for the visitors. However, the Spaniard's attempt from inside the box on the right ended in the side netting.
Pune FC kept on pushing ahead but were falling short of penetrating into the Kitchee box.
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Pune FC first went close in the 22nd minute when Ralte's header off Anthony D'Souza went just over the horizontal. Five minutes later, left-back Gurjinder Kumar beat the offside trap on the left flank to set free only for his directionless cross to go wide.
Into the final five minutes of the half, Pune FC had a glorious chance to open scoring after Mirjan earned a freekick on the edge of the box. However, Anthony's dipping shot went inches over the horizontal.