Alfreton recorded just their third away Blue Square Bet Premier win of the season at Lincoln.
The Imps' Tyrone Thompson and Jefferson Louis both forced saves from Town keeper Jon Stewart early on.
But the visitors took the lead when midfielder Jake Moult found the back of the net with a neat finish for his first goal since Boxing Day.
Substitute Jamie Taylor was denied by Stewart as the hosts pushed for an equaliser, but it was not to come.
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Lincoln City manager David Holdsworth told BBC Lincolnshire:
"It's a disappointing result and very frustrating. I won't say we've battered them but we've been the better team.
"I care about this club, the fans, everyone involved with this club, but we've got seven or eight boys who are on very little money. They're honest and I'll take that any day but if you can't keep a clean sheet you won't win a football match.
"Alfreton are lucky to go home with a win but they've taken the points and we have to look at why we keep conceding and certain people have to stand up and be counted. If they're not up for the fight, they won't play.
"I'm fuming. I'm sick to death of letting in soft goals, but when you have weak mentalities sometimes it frustrates the life out of me and we need to deal with it."
Alfreton manager Nicky Law told BBC Radio Derby:
"We've come here minus Adam Quinn, Greg Young, Anton Brown and Leigh Franks and so we were bare bones again, but we brought two loan players in this week and I thought we started well.
"To lose Theo Streete was a massive blow and Seamus Conneely from Sheffield United has come on and read the game very well and we're delighted to have won it.
"It's always going to be hard coming here, because they're a big side. Normally we're big too, but we were missing a few today. But it was a great time to score because we went in elated and I think it knocked the stuffing out of them a bit."