Ali Fuseini's header secured Lincoln only their second win of the season at the expense of high-flying Gateshead.
The hosts controlled the early stages of the game, Gavin McCallum saw his shot cleared off the line by James Curtis, while Kyle Perry headed wide.
Gateshead, who went into the game as league leaders, went close in the second half through Josh Gillies.
The winning goal came 13 minutes from time, as Fuseini met John Nutter's left-wing cross.
Lincoln move out of the Blue Square Bet Premier relegation zone, while Gateshead slip to third.
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Lincoln City manager Steve Tilson told BBC Lincolnshire:
"It could have gone either way but we got a little break and hopefully we can push on from this.
"The win should give them a massive lift. They're a great bunch of lads that want to do well and that's the difference from last year.
"The lads are buzzing and hopefully it'll continue on to Saturday."