Ethiopian striker Fikru Teferra Lemessa and Czech Republic midfielder Jakub Podany scored for the visiting team who consolidated their position at the top of the standings with six points from two matches but also had Spaniard Borja Fernandez expelled in the 84th minute for receiving two yellow cards.
It was NorthEast United's first loss of the competition after winning their first match 1-0 against Kerala Blasters.
Atletico de Kolkata led 1-0 at halftime through a superbly-taken goal by Fikru in the 13th minute. It was his second goal in as many matches.
The ball was masterly chipped over the NorthEast defence by Kolkata's 'marquee' player Luis Garcia and the striker took it on his chest and volleyed it into the net leaving the vociferous NorthEast crowd stunned. The opening goal was preceded by a strong start from the visiting team.
Atletico de Kolkata led 1-0 at halftime through a superbly-taken goal by Fikru
Spaniard imports Jofre Mateu Gonzalez and Borja came close to scoring, bringing out some fantastic saves from the NorthEast goalkeeper Alexandros Tzorvas, who was kept busy throughout the first half.
Atletico could have extended their lead had the post not come in the way. Jofre's cleverly-taken corner was nodded towards the goal by Botswana midfielder Ofentse Natobut but the ball rebounded off the right post.
The second half was, however, more evenly contest with both teams trying to score and constructing attacks at frantic pace.
NorthEast came close to equalising with 'icon' Joan Capdevilla tapping the ball in the goal in the 70th minute from close range but he was adjudged offside.
As the match wore on, NorthEast asserted their supremacy. Atletico were forced to back off and that pressure forced Borja, who was booked earlier, to commit a needless foul in the 84th minute and get expelled following his second yellow card.
NorthEast committed more men forward but were left vulnerable at the back and Atletico capitalised on the open spaces left behind by their opponents in the final minute of regulation time, executing an accurate counter-attack that was converted smartly by an unmarked Jakub to confirm victory for the Sourav Ganguly-part-owned side.
Atletico de Kolkata next face Delhi Dynamos FC at home October 19 while hosts NorthEast entertain FC Goa on the same day.