Goa took the lead early in the fifth minute through Romeo Fernandes and sealed the victory in injury time courtesy substitute Miroslav Slepicka for their win of the tournament.
With today's win, Goa have 12 points from 10 matches, the same as Mumbai City and FC Pune City but are fourth on better goal difference.
The visitors were denied the equaliser by rival keeper Jan Seda, who made a couple of good saves. Pune were unlucky in the second half which they dominated.
The Pune side made three changes with Dudu Omagbemi, Lenny Rodrigues and Mehrajuddin Wadoo replacing Davide Colomba, David Trezeguet and Israil Gurung.
The hosts, seeking a crucial win to stay in hunt for the semifinals, started offensively and forced the rival keeper Arindam Bhattacharya to make two saves.
The lead was taken as early as the fifth minute when Fernandes guided the ball into the net with a glancing header.
After the goal, the Goans adopted defensive approach and preferred to attack on counter, allowing their opponents to dictate terms in the midfield.
Pune were all over the rivals' citadel as they made series of raids in search of the equaliser but the rival defenders and Seda stood firm to deny them a goal. The visitors were unlucky when Kostas Katsouranis bicycle kick hit the cross bar.
Against the run of play, Goa found their second goal in the third minute of the injury time when substitute Shaikh Jewel floated the ball into the box for substitute Clifford Miranda, whose diving header hit the ground and bounced to substitute Miroslav Slepicka, who headed it into the net.
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