Chester's seven match unbeaten run was ended by the 26th minute header by Northampton's top scorer who was bagging his 24th goal of the season.
The victory means Colin Colderwoood's men are ending the season on a high and could even lift the title in a week's time as they are currently on the back of an eight-match unbeaten run going into their finale at Grimsby next Saturday.
As the golden moment arrived from a long throw by David Hunt which went beyond the far post where McGleish stooped to beat Chris MacKenzie with his header.
MacKenzie who started his career just up the road at Corby spent the rest of the afternoon defying the home forwards and ensuring the promotion was uncertain until the final whistle.
MacKenzie had already made one excellent block from McGleish before the goal and after the break he was at full stretch to tip away a spectacular lob from wide on the right by Andy Kirk.
In a frantic few minutes Chester's Jake Edwards has a volley deflected wide at the other end before Northampton hit back with Martin Smith again bringing out the best from Mackenzie with a stinging left foot volley.
The Chester keeper then denied Kirk from close range before David Rowson saw his header cleared off the line by Steven Vaughan.
Chester had chances to delay the Cobbler's promotion with Edwards badly off target with a close range header while a Ben Davies volley was securely handled by Harper whose clean sheet was the clubs 23rd in the league this season.
It was fitting McGleish should prove the match winner as he was named the club's player of the year before the game.