Goals from Steve Claridge and Nathan Tyson gave the Choirboys the win, and sees United remain in second.
A win would have taken the Iron to the top of the table, but instead there are only three points between United and fourth-placed Macclesfield Town - who are the in-form team of the division without a loss in six games.
Northampton moved up to sixth in the table, replacing Lincoln, with a goalless draw at Notts County.
Cobblers hot-shot Scott McGleish was guilty of a series of glaring misses in a lack-lustre encounter at Meadow Lane.
Both teams lacked a killer touch, mustering just three efforts on target between them. And it was McGleish who squandered the better chances.
His worst miss came on 77 minutes when substitute Stuart Noble sprinted down the left and put a goal 'on a plate' for the front man.
But from ten yards out, and with just the keeper to beat, McGleish kicked nothing but fresh air.
He also missed with two headers in quick succession just before the break - the first from Luke Chambers' cross that flew over the bar.
And when he cleverly worked space from David Rowson's corner at the back post, he nodded another decent chance wide.
In the LDV Vans Trophy southern final first-leg Southend United, fifth in League Two, beat Bristol Rovers 2-1.
They left the Memorial Stadium with a one-goal advantage but feeling that Rovers had gifted it to them.
For the first half-hour the home side used just one attacker; Junior Agogo, and stayed with that system long after Lawrie Dudfield had headed the visitors in front.
The build-up came when Rovers' Ryan Williams lost the ball on the halfway line and Lewis Hunt ran clear down the right to find Dudfield with an accurate centre.
The home side had the chance on the half-hour to pull this goal back when Spencer Prior upended Craig Disley but Agogo slammed the penalty against the bar.
Rovers drew level ten minutes into the second half with Richard Walker gliding in a header from a deep Stuart Campbell corner.
Southend were back in front 12 minutes later with Mark Gower cutting in from the left and hammering a shot in off the underside of the bar.
In the LDV Trophy northern final first leg Wrexham outgunned Oldham 5-3, with Juan Ugarte blasting a hat-trick.