Stuart Dallas came off the bench to score for the Cobblers as they won away from home for the first time this season.
The Northern Ireland international, whose arrival on loan from Brentford was kept a secret until an hour before kick-off at Wimbledon, was joined on the scoresheet by Lee Collins, who put in a good shift in a new role as a holding central midfielder.
Collins’ goal, a fine volley from Darren Carter’s free-kick, represents the first away goal of Northampton’s season and Dallas put the seal on their first away win, by a 2-0 scoreline, with a slick finish after being introduced as a second-half substitute.
The Cobblers lined up with a new-look formation that saw Collins used as a holding midfielder in front of a conventional back four in which Joe Widdowson was recalled at left-back.
Collins was involved right from the start, looking to press Luke Moore whenever he found pockets of space in the Dons’ advanced midfield areas.
Wimbledon enjoyed a couple of brief flurries across the Town box before the visitors had their first meaningful attack 20 minutes in, Carter seeing his volley blocked away for a corner after a break down the left.
Carter then provided the game’s first goal with an expertly-delivered free-kick which Collins met with perfect timing and an even better finish, rattling home on the angle with his right foot.
Spurred on by their first away goal of the season, Chris Hackett then created space in typical style down the right and delivered a cross that Ian Morris headed over when he really should have at least got the effort on target.
Town had the ball in the back of the net on the half-hour mark when Gary Deegan hit a volley that deflected - against an allegedly offside Roy O’Donovan - and span into the net via the outstretched hand of home keeper Ross Worner.
Wimbledon repeatedly got into good areas but their crosses were cleared with a degree of comfort by the Cobblers defence - time and time again, Mathias Doumbe and Paul Reid positioned themselves perfectly to clear the danger with Collins usually on hand to pick up the loose ball.
Stuart Dallas was introduced on the hour-mark, on the right of midfield in place of Hackett, and he enjoyed a couple of bright early moments with a neat cross and a shot that drifted wide of the target.
He dug out a fine left-footed cross from deep on the right wing that Morris met with a firm header at the back post, but one that was into the ground and wide of the mark.
Like the one in the first half, he probably should have done better with it but it did not prove costly.
The Dons mounted a brief spell of pressure that abated when Duke took a corner cleanly and thumped the ball upfield where it was controlled on the first bounce by Roy O’Donovan.
The Irishman, who had played a slide-rule pass into Dallas moments before, did so again and this time the Brentford loanee opted for the direct route, running straight at Worner and drilling the ball underneath him.
Dallas then smacked a left-footed effort narrowly wide of the target after initially creating space for the break down the right wing.
Two was enough, although Duke had to make a low save in injury-time to keep out an exocet of a free-kick from Harry Pell after Collins was harshly adjudged to have fouled Sammy Moore.
Wimbledon: Worner, Fuller, Kennedy (Midson 60), Frampton (Fenlon 46), Bennett, Francomb (Arthur 46), Pell, S Moore, L Moore, Smith, Porter
Subs not used: Weston, Brown, Sweeney, Beere.
Cobblers: Duke, Amankwaah, Collins, Doumbe, Reid, Widdowson, Hackett (Dallas 57), Deegan, Carter, Morris, O’Donovan (Toney 82)
Subs not used: Demontagnac, McNamara, Emerton, Harriott, Dallas
Away fans: 398
Referee: Andy D’Urso