The visitors enjoyed their fair share of chances, but John Marquis' fourth goal in seven games was enough for Cobblers, with the on-loan striker converting Lee Martin's cross from close range in the 22nd minute.
Second-placed Oxford played 75 minutes of their 1-1 draw with Stevenage with 10 men but should still have been celebrating maximum points.
The U's were reduced to 10 men when midfielder John Lundstram dived in on Michael Tonge.
League Two
AFC Wimbledon beat Plymouth to secure League One promotion
30/05/2016 AT 13:22
But they were gifted the chance to take the lead just before half-time when Stevenage goalkeeper Jamie Jones wrestled Danny Hylton to the ground in the penalty area. Jones redeemed himself, however, saving Liam Sercombe's spot-kick.
Sercombe did grab the opening goal in the 58th minute, bringing down a cross from Kemar Roofe and side-footing in but Stevenage levelled after 69 minutes when Byron Harrison slotted home Greg Luer's lay-off.
Bristol Rovers stay third after a comfortable 3-0 win at home to Cambridge.
Billy Bodin scored twice in the opening 18 minutes and Matty Taylor secured the points with a coolly-taken 22nd goal of the season.
Accrington are still in the hunt for automatic promotion following a 1-0 win against Leyton Orient.
After a goalless first half, Stanley grabbed the winning goal early in the second as Billy Kee's chested lay-off allowed Scott Brown to drive the ball home.
Portsmouth cruised to a 4-0 win as Mark Cooper endured a nightmare start to life in charge at Notts County.
Pompey broke the deadlock on the stroke of half-time when Kyle Bennett burst down the left wing and into the area before finishing under the goalkeeper.
And Bennett made it two after 49 minutes when he kept his cool one-on-one to slot the ball past Scott Loach.
Christian Burgess' thumping header made it 3-0 and Marc McNulty added a fourth in time added on.
Wycombe moved into the play-off places after Michael Harriman's superb strike earned them a 1-0 win against Mansfield.
At the bottom, York remain seven points adrift of third-bottom Stevenage after they were held to a 2-2 draw at home by Crawley.
The Reds took a fifth-minute lead through Matt Harrold's neat flick finish over the goalkeeper.
Luke Summerfield levelled from the penalty spot on the half-hour after Lewis Alessandra had been brought down in the area.
But Crawley regained the lead at the start of the second half when Liam McAlinden's scuffed shot had enough to beat Scott Flinders.
York were back on level terms again after 69 minutes when substitute Michael Coulson curled a superb shot into the top corner and the game ended all square.
Hartlepool are now 11 points clear of the relegation zone as Adam Jackson nodded in the only goal of a 1-0 win over AFC Wimbledon at Victoria Park.
They are level on points with Yeovil, who played out a goalless draw with Carlisle.
Elsewhere, Jayden Stockley scored his third goal in as many games to put Exeter in front against Barnet, heading in Matt Oakley's long ball forward.
But the home side's joy was short-lived, with Curtis Weston making it 1-1 six minutes later with a close-range header from Elliot Johnson's cross.
Plymouth's game at Morecambe was delayed by half an hour due to traffic congestion on the M6, but the visitors claimed a 2-0 win to keep in touch with the top three.
They took an early lead when Jordan Houghton, on loan from Chelsea, sent a controlled drive into the bottom corner from the edge of the box.
Morecambe were reduced to 10 men in the closing stages of the first half when Alex Kenyon lunged in on Carl McHugh.
And Jamille Matt extended Plymouth's lead at the start of the second half, collecting a Jake Jervis pass and drilling home.
League Two
Penalty levels League Two play-off first leg between Portsmouth and Plymouth Argyle
12/05/2016 AT 21:36
League Two
Oxford and Bristol Rovers grab promotion as Accrington Stanley blow it
07/05/2016 AT 16:51