Wesley York's dramatic injury-time winner earned Nuneaton a vital win in their fight to avoid relegation over fellow strugglers Lincoln.
York unleashed an unstoppable strike in the 93rd minute to move Boro within a point of their opponents.
The hosts could have opened the scoring in only the second minute, but Gareth Dean's effort was blocked.
Nathaniel Brown had the visitors' best chance, but he headed straight at Nuneaton goalkeeper Lee Burge.
The Imps now lie just one place above the relegation zone after their third defeat in four outings.
Sixty people were arrested for violent disorder before the match.
VIEW FROM THE DRESSING ROOM
Lincoln City manager Gary Simpson told BBC Radio Lincolnshire:
"It was a great strike, to be fair, and it was going to take something like that to win the game. Conditions were difficult, it wasn't a great spectacle and draw would have been a fair result but a wonder strike in injury time has cost us again.
"It is a tough defeat to take and everybody is disappointed. It was a game we thought we could get something out of and it looked like we would get something from it, but when you're down there these things come to kick you and it's how we react to it.
"We're not going down without a fight, there's no two ways about it. At times it seems like everything's against you but it's about sticking together and coming out fighting."