This was Chennaiyin's third home loss at Jawaharlal Nehru Stadium to dim their semi-final hopes after being undone in their second encounter against NorthEast United.
Chennaiyin though started on the right foot as Elano helped take the lead for the hosts in the 33rd minute.
NorthEast's Cameroonian defender Andre Bikey headed a cross away from the penalty area but the ball fell nicely at the feet of Elano.
The Brazilian great though still had to do the hard work to get his shot away on target and the skipper sent a superb volley down the bottom left. NorthEast goalkeeper Rehenesh had no chance as the strike was destined for the back of the net.
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Bruno sent in a good cross at the far post for Kamara and the forward headed it straight at the keeper in the 44th minute. Apoula only managed to punch it back to Kamara and he gleefully slotted the ball into the back of the net from the point blank range.
The teams headed into half-time locked at 1-1.
The battle resumed after the break with the pendulum swinging from one goal to another.
But it was the second change for NorthEast that made it count as Portuguese midfielder Silas, who came in for Simao, gave the visitors the winning strike in the 72nd minute.
The strike gave the visitors the lead and it finally proved decisive as the hosts not only failed to score in 90 minutes but their efforts were neautralised even in the four extra minutes of injury time.
The win has made the visitors jump to fifth position and are behind Atletico de Kolkata only on goal difference.