Lallianzuala Chhangte (41st) broke the deadlock with a powerful shot from a defensive error but VP Suhair (50th) restored parity before Chennaiyin captain Anirudh Thapa (74th) sealed the deal with a fine strike.
The win took the two-time champions to second spot with six points from two matches.
Thapa latched on to a ball from Rahim Ali and slotted it past the NorthEast United custodian.
Apart from a moment where it seemed Chhangte had beaten Subhasish Roy Chowdhury's nearside to squeeze a goal, it was all NorthEast in the opening exchanges.
Federico Gallego's quality was on display as he peppered the Chennaiyin defence several times. VP Suhair and Laldanmawia Ralte too had a few sniffs in the opposition box to keep the Highlanders on top.
Unfortunately, Gallego could only last 24 minutes as he pulled up injured yet again. NorthEast United, already missing the services of Deshorn Brown in the game, had to put in Pat Flottmann, going in for an added defender.
The game was thrown open with chances at both ends. Suhair's header from a long throw-in was saved by Vishal Kaith and then Hernan Santana's long-ranger went inches above.
Chhangte, who had earlier blazed over the bar, made amends before half time. After some exquisite counter-press through the right, Reagan Singh squared the ball into the box. Khassa Camara mistimed his interception and Chhantge pounced onto the ball to slot it home after a deflection off the bar.
Khalid Jamil made two changes post the break and results immediately showed. Five minutes in, VP Suhair, relatively unmarked, had no problems in guiding the ball past Vishal Kaith from a long-throw in by Provat Lakra. NorthEast had found the equaliser with more than 40 minutes to go.
Lalkhawpuimawia shot wide despite having an empty net to aim at. Gurjinder Kumar's long ranger took a deflection off Slavko Damjanovic and ricocheted off the post. With Kaith, yet again out of position, the Mizoram-born striker failed to hand his team the lead.
Post the hour mark, Mirlan Murzaev found the back of the net but Rahim Ali's through ball to the Kyrgyz was deemed offside.
It was then the new captain Thapa to have his final say in the game.
Murzaev laid in the midfielder from a long ball. Thapa sprinted full pace to go past marker Camara and shoot fiercely to restore the lead, crucially closing the game for Chennaiyin FC.