And the result blew rock bottom Rotherham's chance of wiping out the pre-season 10-point penalty imposed by the league at the end of last season.
Dave Hibbert claimed his first goal for the Millers with a seventh minute header from Delroy Facey's cross but Northampton always looked a threat.
And the home side squandered a glorious chance to seal the win when Ritchie Patridge was fouled by Luke Chambers in the area after 71 minutes. Mark Bunn saved Michael Keane's sloppy spot-kick.
Then three minutes later McGleish pounced to fire in the equaliser from Andy Kirk's assist. And eight minutes from the end McGleish rose unchallenged to head in a free kick from Eoin Jess.
Rotherham went ahead when Facey's header was blocked out. Facey chased the loose ball and hooked it back into the area where Hibbert rose to head it past Bunn.
The goal was a setback for Northampton who had shown more enterprise in the opening minutes but they continued to play neat and tidy football in midfield looking to create an opening.
However it was Rotherham who threatened to add to the score on the break when German midfielder Eugen Bopp lashed a rising shot from 20 yards that drifted over.
The visitors produced their first meaningful threat after 22 minutes when Kirk rounded off a sharp move with a low drive from 20 yards but Neil Cutler made a comfortable save.
In the dying minutes of the first half Northampton might have levelled.
Jess swung in a pin-point corner and centre-back Sean Dyche leapt above the Rotherham defence to produce a towering header. He should have hit the target but instead guided the ball just wide of the target.
And in 71 minutes Rotherham blew the chance of bagging the three points with a missed penalty. Chambers barged into Partridge but Keane's penalty was easily saved.
Three minutes later the visitors were level. Kirk hooked the ball across the face of goal and McGleish crashed in the shot.
And in the 78th minute Jess hit the post and Kirk lifted the rebound over the top.