Torquay extended their winning run to five matches against Northampton.
Luke Gutteridge went close to putting the League Two strugglers ahead in the first half but his 20-yard shot was saved by Gulls keeper Bobby Olejnik.
The midfielder then saw a close-range effort go wide after he had dived to try and convert Michael Jacobs' cross.
But it was the hosts who broke the deadlock as defender Mark Ellis powered a header home for his third goal in four matches to edge the win.
It was tough on visiting defender Kelvin Langmead, who had earlier made a great diving block to deny Chris Robertson from point-blank range.
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Torquay United manager Martin Ling told BBC Radio Devon:
"There was a purpose to us in the second half.
"What I would like to do is turn my phone off until 11 o'clock on Tuesday and have no bids for any of our players.
"The players are very confident at the moment."
Northampton Town manager Aidy Boothroyd tells BBC Radio Northampton:
"We're bottom of the table because we can't keep a clean sheet. It's as simple as that.
"It's one second of indiscipline that costs you. And those are the margins between being a really good team or a really average team.
"We're too soft but we'll change that and make sure that we get ourselves out of where we are.
"I'm annoyed about it because we've done so well. When you get so near and yet so far, it's galling."