Darlington were aware that they required a victory against their high-flying visitors and, after an edgy opening period to the game, it was the hosts who had the first clear cut opportunity in the 16th minute.
Winger Simon Johnson gained some space on the right flank and his cross found striker Andy Cooke inside the box. Cooke made space for himself with a quick turn and his shot was well collected by Lee Harper in the Town goal.
As play switched from end to end Darlington keeper Sam Russell raced out of his goal after a back header from Matty Appleby put the keeper under pressure in the 17th minute.
The game was becoming more open at this stage and the home side again threatened when a long clearance found Cooke in the area on 21, but with only Harper to beat, he totally mis-cued and the ball went out for a throw-in for the visitors.
Northampton came back into the game and had two good chances in the 25th minute. The first fell to Martin Smith, but he was denied by Russell who did well to charge down the shot at the near post and then, seconds later as the Quakers defence back tracked, the ball again found Smith who beat Russell with a rising 20-yard drive which struck the post.
In the 28th minute Darlington should have scored through Jonjo Dickman. Simon Johnson found Dickman in the area and, with the goal at his mercy, he somehow miss kicked and the ball was cleared.
Northampton again struck the woodwork on 33 when defender Chris Doig powered a header against the bar. From the rebound the normally reliable McGleish shot wide at the far post.
The visitors almost scored on 50 minutes when Josh Low dispossessed Darlo captain Matthew Clarke inside the area, but Clarke recovered with a last-ditch tackle that blocked Low's effort.
The visitors made a double substitution on 65 when Eoin Jess and the impressive Gavin Johnson were replaced by Andy Kirk and Ashley Westwood. The changes had an almost instant impact as the visitors took the lead just three minutes later.
Low sped down the right and sent over a low cross that somehow eluded the Darlington defence and McGleish was left with a simple tap in at the far post that proved to be a winning strike.