Taken apart by top-of-the-table Forest Green Rovers in midweek, the Sulphurites produced a much-improved overall performance and matched the Cobblers for the majority of a freezing cold Saturday afternoon.
Far more solid at the back in open play, they were however caught out twice at set-pieces, meaning that Jack Diamond's 24th-minute stunner would ultimately count for nothing.
Town survived an early scare when Sam Hoskins curled a 25-yard free-kick against Mark Oxley's right-hand upright with the Harrogate custodian rooted to the spot.
But, with just seven minutes on the clock, they found themselves trailing for the sixth home game in succession.
Mitch Pinnock delivered a corner from the right and it was all too easy for Fraser Horsfall to meet the ball at the far post and help it into the net from just a few yards out.
Having collapsed and conceded three times in the space of 24 minutes before half-time during their heavy defeat to Forest four days earlier, it was imperative that Town stayed in the contest on this occasion.
And, while there were plenty of panicky clearances and aimless punts forwards in the period that followed the Cobblers breaking the deadlock, Weaver's men did indeed manage to hang tough and avoid further damage.
And, almost straight off the back of their first decent passage of play of the match, the hosts got back on level terms.
Diamond, who had been the only player in yellow and black to impress up to that point, came inside off the left, travelled across the edge of the penalty area and blasted a fine right-footed finish into the top corner.
Energy and belief suddenly coursing through the veins of the home players, the momentum of the game shifted. Alex Pattison saw a tame effort easily saved, then Luke Armstrong hit the back of the net from close range, though the offside flag has long-since been raised.
Some excellent pressing by Pattison then saw him dispossess Horsfall and play Armstrong in on goal, his initial strike saved by Roberts before Thomson's goal-bound follow up was blocked by a scrambling defender.
Having finished the opening 45 firmly in the ascendancy, Harrogate almost conspired to gift their visitors a second goal within four minutes of the resumption.
Thomson's suicidal attempted back-pass afforded Nicke Kabamba a clear run on goal, however Oxley came off his line, made himself big, and produced a solid one-on-one save.
Sixty seconds later, he was however beaten for a second time, Jon Guthrie climbing well to nod home from Pinnock's inviting free-kick from the right.
With plenty of time to get themselves back in it, the Sulphurites probed away in search of a second leveller, though they failed to really worry the Northampton back-line.
Indeed, a fourth goal of the afternoon looked more likely to arrive at the opposite end of the field where Kabamba forced a parry out of Oxley and Danny Rose cleared the cross-bar with a spectacular bicycle kick.
The introduction of Ryan Fallowfield at right-back added some much-needed impetus down the right, however nothing resembling a clear goal-scoring opportunity presented itself and the Cobblers were able to see the game out with relative ease.
Defeat sees Harrogate drop one place to 10th in the League Two standings.