Cobblers suffered their first home league defeat of 2016 when conceded a last-gasp goal to lose 3-2 to Bristol Rovers after an action-packed affair at Sixfields on Saturday.
A first-half short on both quality and drama was livened up by Alex Revell's wonderful eighth-minute finish that had the Cobblers in front at the break, but a low-key opening 45 minutes was then to make way for a chaotic second-half.
Rovers came out flying after half-time with Rory Gaffney's deflected strike bringing them level before Peter Hartley headed the rampant visitors into what was at that point a deserved lead.
But back came Northampton as second well-taken goal by Revell brought the home side level and set up a frantic, end-to-end finish to the game.
The visitors always looked the more likely to win it, though, and that they did with Charlie Colkett's low finish in the second minute of injury time.
The defeat is just Town's second of the season and if truth be told, it was a deserved one, their misery compounded by a late red card to Gabriel Zakuani just prior to the visitors' winning goal.
The Cobblers had looked relatively comfortable up until half-time but Rovers went through the gears in the second-half and were devastating on the break, with Adam Smith having to be at his best to keep his side in the game.
Despite the result, Northampton only drop one place to fifth in Sky Bet League One.
Cobblers were unchanged from Tuesday's 3-1 win at Swindon Town and they didn't need long to get back into their stride against Rovers, requiring a mere eight minutes to break the deadlock.
The goal all started from a chance for visiting striker Ellis Harrison whose acrobatic volley was held by Smith, and the Northampton goalkeeper proceeded to launch downfield where Revell somehow escaped the attentions of the Rovers defence to find himself clean through.
Faced by the onrushing Kelle Roos, Revell kept his cool to send a superbly-judged lob over the visiting keeper and into the bottom corner, giving his side the perfect start.
Rovers responded with a period of pressure as Northampton sat back and allowed their visitors to knock the ball about, a tactic which nearly backfired on 18 minutes when Gaffney teed up Ollie Clarke for a shot that was dragged wide from 18 yards.
That was one of very few sights of goal in a scrappy, disjointed opening 45 minutes that was constantly punctuated by the noise of the referee Graham Horwood's whistle.
Neither side were able to find any fluency or urgency as Northampton stoutly defended their slender 1-0 lead, an advantage that could have been more comfortable at half-time had Sam Hoskins' first-time effort from Brendan Moloney's drilled cross hit the other side of the net.
Trailing 1-0 at half-time, Rovers made a lively start to the second period and twice came close to levelling when Smith parried Harrison's cross-shot clear and Zakuani blocked the follow-up attempt.
The visitors were on the front foot and came even closer to a second goal when counter-attacking from a Northampton corner, only denied by a brilliant Buchanan block, before Matty Taylor headed off the line in a frenetic passage of play.
Rovers were getting closer and closer to pulling back on level terms, and it came as no surprise when they eventually did equalise.
Northampton had been warned several times but they still couldn't prevent the visitors from scoring when Gaffney's cross took a wicked deflection off Taylor and flew into the roof of the net.
Rovers now had all of the momentum and were coming forward with regularity and another terrific goal-saving block from Zakuani stopped Gaffney from putting his side back in front.
But the Pirates had now wrestled almost total control of the game and their surge was unrelenting with Town struggling to keep them at bay.
With the introduction of top scorer Matty Taylor, Rovers were the only team who looked like winning it, and they had the lead their second-half dominance had warranted when Smith failed to keep out Peter Hartley's powerful header from a corner.
However, that appeared to kick Town back into life and despite being outplayed for much of the second period, they struck back and levelled within five minutes.
Substitute Kenji Gorre played an integral role in the goal when he lead out a breakaway, drove at the Rovers defence and slipped through Revell who again remained composed to slot past Roos for the second time of the afternoon.
With 14 minutes remaining, the three points were anyone's for the taking and Rovers seemed certain to go back in front when Gaffney produced a fine piece of skill to get away from Diamond and fire towards the bottom corner, but Smith pulled off stunning low save.
Then it was Northampton's turn to go close as Gorre sent a 30-yard blockbuster towards the top corner but Roos tipped behind
There was then a brief delay for an injury to referee Horwood, and the first act for new whistler Josh Smith was to show a red card to Zakuani for bringing down Taylor right on the edge of the penalty box.
Colckett's subsequent free-kick was brilliantly turned behind by Smith but Rovers were not to be denied an injury-time winner.
In the second of six added minutes, Colkett was left unmarked inside the penalty box and he made no mistake, drilling a low shot through the legs of Smith.
Northampton had nothing left to give despite their best efforts and they duly fell to defeat, something of a rarity in 2016.
Cobblers: Smith, Moloney, Diamond, Zakuani, Buchanan, O'Toole, Taylor, Hoskins (McCourt 84), Beautyman (Richards 64), Anderson (Gorre 66), Revell
Subs not used: Cornell, Nyatanga, Sonupe, Hooper
Rovers: Roos, Roberts, Lockyear, Hartley, Brown, Lines, Clarke (Moore 55), Sinclair (Bodin 55), Colkett, Harrison (Taylor 67), Gaffney
Subs not used: Mildenhall, Clarke, James, Clarke-Salter
Referee: Graham Horwood
Rovers fans: 997