Goa were at the receiving end of a series of NorthEast onslaught after Sahil Tavora was sent off in the 72nd minute for his second bookable offence and the match locked at 1-1.
But in a dramatic finish, Romeo Fernandes scored the match-winner with just a few seconds left into the four-minute injury time to the wild celebration of home fans.
With the win, Goa broke their winless streak at home to notch up their third victory and take their tally to 10 points, the same as NorthEast and Chennaiyin FC, but still remain at the bottom of the league table on inferior goal difference.
Seityasen Singh put NorthEast United ahead in the 49th minute but Robin Singh cancelled the lead in the 62nd minute.
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As four foreigners in the team could not play due to suspension and two others injured, FC Goa had no option but to field nine Indian players and two from abroad. The home side faced a barrage of attack from their opponents who too need a win badly after three consecutive losses.
Goa managed to keep their slate clean largely due to the outstanding performance of goalkeeper Laximikanth Kattimani who brought off several smart saves.
The home team tried to attack from the flanks but could not threaten their opponents as their final passes went astray.
NorthEast scored soon after the resumption. Following a corner kick by Katsumi Yusa who floated the ball into the goalmouth, Robin cleared the ball with his head. The loose ball went to Seityasen who controlled the ball, then swivelled before essaying a firm left-footer that took a deflection of a defender and beat keeper Kattimani all ends up.
The goal enliven the match as both the sides went on the attack and Goa citadel survived in the 69th minute when Nicolas Velez saw his volley saved by keeper Kattimani off a cross from Holicharan Narzary.
Goa were reduced to 10 men in the 72nd minutes when Sahil Tavora got his second yellow for a foul on Narzary near the edge of the box. With the numerical superiority, the visitors pressed hard in search of the winner but keeper Kattimani did well to save a powerful shot from substitute Koffi Ndri.
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