The Cobblers suffered their fifth defeat in six games as Plymouth Argyle recorded what should have been a comfortable win at Sixfields but one which they were forced to hang onto in its final stages.
First-half goals from Peter Hartley and Andy Kellett put the Pilgrims on the march and Lewis Alessandra added a third midway through the second period.
Ivan Toney scored with 11 minutes to go to spark an attempted comeback and Stuart Murdoch’s sizzling shot breathed further life into it with the scoreline 3-2 going into four minutes of added time.
Town had a couple of chances during that but ultimately came up short and succumbed to another home loss.
Northampton had kept clean sheets in their three home games prior to this one but were behind after only four minutes, Hartley evading Ben Tozer to thump a header past Duke at a corner.
Against the team with the best division it was going to take something special for the Cobblers to get back into the contest but they reacted positively to conceding and Darren Carter had a full-blooded shot blocked on the edge of the box.
Kaid Mohamed then did well to pick out Marc Richards from the left wing but, with his weaker left foot, his shot was a wayward one.
Plymouth were as unadventurous as you would expect an away team with a lead to be, but almost scored after a Lee Collins slip presented Reuben Reid with a clear run at goal, Matt Duke making the low save to keep his eventual shot out.
Carter and Ollie Banks got in each other’s way when attacking a right-wing cross on the half-hour mark but shortly afterwards Plymouth scored their second.
Some will hail it as an excellent piece of individual play but there wasn’t a challenge in sight on Kellett, who strolled through the home team before tucking his shot into the corner.
Chris Wilder rolled the tactical dice at half-time, putting on Emile Sinclair and Ivan Toney in place of his wingers, and then introducing Lawson D’Ath 10 minutes into the second half.
But within moments of the final substitution, Plymouth had their third goal with Alessandra seemingly having all the time in the world to take touch after touch in the box before drilling a shot past Duke.
Toney gave what remained of a frozen and almost mutinous home crowd something to cheer when he tapped in his seventh goal of the current campaign.
There were 10 minutes of normal time on the clock at that point and with two to play Murdoch swirled in an excellent dipping shot which beat goalkeeper Luke McCormick all ends up.
An almighty spell of pressure then followed, in which Kelvin Langmead had two efforts blocked at close range before the ball was eventually cleared to safety.
Toney almost scored an equaliser in the final minute of added time with an overhead kick which drifted just wide of the target and then sliced another shot over the bar.
Cobblers: Duke; Tozer, Langmead, Collins, Robertson; Hackett, Murdoch, Carter, Mohamed; Banks; Richards
Subs: Sinclair (for Mohamed 46), Toney (for Hackett 46), D’Ath (for Banks 56)
Not used: Alfei, Horwood, Diamond, Ravenhill
Plymouth: McCormack; Nelson, O’Connor, Hartley; Mellor, Cox, B Reid, Blizzard, Kellett; R Reid, Alessandra
Subs: Norburn (for Blizzard 38), Banton (for Alessandra 70), Harvey (for R Reid 76)
Not used: Bittner, Purrington, Banton, Allen, Bentley
Away fans: 565