David Williams had put ATKMB ahead with a well-taken goal early on in the first half, but Antonio Habas' side failed to make the most of their early advantage.
The second leg will take place on Tuesday, and the game will go to extra time, and penalties, if the aggregate score remains tied. The result also meant Khalid Jamil is still unbeaten in the competition and extended NorthEast's unbeaten run to ten games.
NorthEast dominated possession in the first half, but Bagan scored with their first shot on target soon after the water break. Roy Krishna received a long ball at the edge of the box and flicked it to his strike partner Williams, who faked a first-time shot sending NEUFC defender Dylan Fox in the wrong direction. He then took a touch before slotting it into the bottom right corner with a left-footed effort to give ATKMB an advantage.
NorthEast came agonisingly close to scoring but were denied by the woodwork. Federico Gallego delivered a great freekick in to the area where Ashutosh Mehta leapt high, only for his header to clatter against the crossbar. That was the closest NEUFC came to scoring in the first session.
ATKMB defended deep in the second half, but were lucky not to see a man being sent off. Luis Machado, while chasing a long ball outside the area, was taken out by onrushing Bagan keeper Arindam Bhattacharja. However, the referee waved off any appeal for foul though replays suggested the keeper made contact with Machado.
NorthEast had a constant supplier in Gallego, who sent quality deliveries into the box from set-pieces but his teammates couldn't find a finish. Meanwhile, Prabir Das had a couple of decent attempts. While one was easily swallowed up by Subhasish Roy, the other sailed over the bar.
Jamil introduced Idrissa Sylla and Britto PM in a bid to get the equaliser, and they kept stitching passes together, but the ATKMB remained tight at the back.
NorthEast had a couple of chances late in the game. But Fox saw his header cleared by Pronay Halder, while Sylla's long-range effort failed to trouble Arindam.
In the fourth minute of extra time, the NorthEast camp had a goal to celebrate, thanks to Sylla who made his presence felt with a late equaliser, nodding in Luis Machado's cross.
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