Lajong pumped in two quick goals through Saihou Jagne (13th) and Abdoulaye Koffi (18th) and the home side, who were aiming to win this match to top the league table, could not score despite having several chances in the eleven round game.
Neroca, who were playing in their debut season, dominated the whole of the second half with better ball possession and also created several chances but their forwards were found wanting in front of the goal.
Their defence, which has been rock solid before this match and conceded just six goals in 10 matches, struggled in the first half an hour, helping the Shillong side to take a 2-0 lead before the 20th minute.
Despite today's loss, their first at home, Neroca still remain on second spot in the league table with 21 points from 11 points. They can top the table if they beat leaders Minerva Punjab FC (22 points from nine matches) at home on January 27.
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Lajong, on the other hand, jumped two places to fourth with 17 points from 12 matches.
Neroca started brightly by putting early pressure on their opponents. They had the first chance of the match in the fourth minute when Nedo Turkovic sent Subash Singh on the clear inside the box but the Manipuri player's feeble attempt was saved by Lajong goalkeeper Nidhin Lal.
The demanding and vocal home crowd was stunned to silence as the visitors struck another blow five minutes later through Koffi. The Ivorian striker jumped higher than Gouramangi Singh to connect a Novin Gurung cross and is header hit the net after hitting the inside of the post with goalkeeper Mistry out of line.
Neroca head coach Gift Raikhan brought in David Lalbiakzara in place of Ronald Singh in the 28th minute in a bid to find goals. David's entry did infuse some urgency but ultimately a goal eluded the Imphal side.
They had lost to Minerva Punjab 1-2 in Ludhiana in their campaign opener on December 1.
In the 50th minute, Nedo Turkovic put the ball into the Lajong net off a free-kick but the goal was disallowed as he was adjudged to have used his arm to guide the ball in.
Turkovic, who scored Neroca's match-winner against Aizawl, was able to get into the box from the right and square it into the path of Felix Chidi but the Nigerian striker's shot in the 73rd minute went wide.
Towards the end of the match, there were frayed tempers with players of both sides pushing and shoving each other near the touchline after a Lajong player charged his Neroca counterpart but the referee did not see it. The referee later handed yellow cards to two Neroca players.
Shillong Lajong assistant coach Alison Kharsyntiew said this win will motivate his players going into the remainder of the league.
"This win will motivate the players because we have not done very well in the league so far. Hopefully, we keep improving and keep winning," he said at the post-match press conference.
Neroca head coach Gift Raikhan took the blame on himself for today's loss.
"Our strategy was not successful. That is my mistake and I take the blame for the loss. I changed the strategy after conceding two goals and it did not work out. Sometimes teams have off days. Because of various reasons, we did not play well in the first half but we played well in the second half but could not get the goal," he said.
Raikhan, however, said the I-League title was still within the reach of his side.
"I said earlier that this team can be champion. I still say that we can be champion. We will learn from today's defeat. I hope today's defeat will be a stepping stone to winning the title," said the former Pune FC assistant coach.
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