Plymouth sealed back-to-back league wins for the first time this season as Lewis Alessandra's late goal condemned Northampton to the bottom of the table.
Argyle defender Curtis Nelson went close at both ends in the first half, heading onto his own post before forcing a good save from Matt Duke.
Luke Norris went closest for the Cobblers, but Pilgrims goalkeeper Luke McCormick made a magnificent save.
Alessandra sealed the win as he took a deft Reuben Reid pass and slotted home.
The goal had been coming for Argyle, who still have the worst scoring record in League Two, with Reid and Alessandra both having gone close before the 90th-minute winner.
VIEWS FROM THE DRESSING ROOM
Plymouth Argyle manager John Sheridan told BBC Radio Devon:
"Just after half-time they had a little spell where we got a bit sloppy and Luke McCormick's had one or two shots to save, which I didn't really like the look of, but after that I thought we created lots and lots of chances.
"The goal to win the game was an excellent move. Youngy's (Luke Young) come on, and I like my subs sometimes to come on and change the game, and I think Youngy's just played four or five passes, which no-one really did in the whole game.
"We're just getting on a little run. Clean sheets are a good habit but our problem has been scoring goals, and the pleasing thing is we could've scored three or four."
Northampton Town manager Aidy Boothroyd tells BBC Radio Northampton:
"It's sickening, and I need to make some changes. It's not acceptable.
"I am really irritated by what I've seen in that last five minutes. You do not concede in the last few minutes.
"There's no point in doing half a job, preparing like we do, working hard all week and then throwing it all out the window because we're not disciplined enough to win a game.
"I'm extremely annoyed at some of the players and I need to do something about it. These players are good enough and yet we are languishing where we are."
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