Rowllin Borges and Bartholomew Ogbeche' scored (4', 33') in the first half and helped the Highlanders pick up a crucial win and move up on the league table to the second position, overtaking Mumbai.
Jorge Costa made two changes to the Mumbai City lineup that went down 0-1 to Jamshedpur last week. A suspended Lucian Goian was replaced by Anwar Ali and Arnold Issoko returned to the first team in place of Bipin Singh.
Pawan Kumar, Keegan Pereira and Gurwinder Singh featured in Eelco Schattorie's starting lineup. TP Rehenesh and Robert Lalthlamuana sat out and Redeem Tlang was dropped to the bench.
NorthEast United came out all guns blazing and took the lead in the fourth minute. Keegan Pereira marauded down the left flank and was afforded space and time to pick out an unmarked Rowllin Borges in the centre of the box with an accurate low cross. The Indian midfielder found the net with a first-time strike.
The absence of Lucian Goian was severely felt as NorthEast United's forwards, Panagiotis Triadis in particular, continued to create problems for Anwar Ali and Marko Klisura.
Mumbai City's only major opening came in the 10th minute when Rafael Bastos was denied a goal by the crossbar. Arnold Issoko ghosted into the box from the right flank and picked out the Brazilian striker whose curling strike from the edge of the box hit the crossbar and went out.
The visitors were afforded space to operate in the attacking third and they took advantage of it to double their lead in the 33rd minute. Federico Gallego released Reagan Singh into space down the right flank and the right-back's drilled cross towards the far post was guided into the net by Bartholomew Ogbeche who scored his 12th goal of the season.
Mumbai City mounted pressure on the opposition's defence after the restart. Sauvik Chakrabarti found space to attack the left flank and forced a decent save off Pawan Kumar at his near post in the 55th minute.
Two minutes later, Raynier Fernandes picked out Marko Klisura inside the box with a ball over the top from his own half. The defender met the delivery with his knee and failed to control his attempt on target.
Mumbai City struggled to make an impact in the final third as the game went on. Arnold Issoko picked out Modou Sougou in the box with a cross from the right and the striker summed up the night's display as he scuffed his shot wide.