It was a miserable night for the Lions who never suggested they would be roaring as their four-match winning streak came tamely to an end while midfielder Alan Dunne was shown the red card in the final minute for a foul on Bradley Johnson.
Millwall will feel aggrieved as they led this match 1-0 when it was abandoned 24 days earlier.
However, their lack of threat was apparent as early as the 37th minute when manager Willie Donachie saw fit to make a double tactical switch to try to introduce some much-needed sparkle.
It took Millwall 51 minutes to manage an effort on goal and, although they then had a short flurry of half-chances, highly-rated Northampton goalkeeper Mark Bunn was scarcely troubled.
There were few chances for either side in the first half, although Andy Kirk went through in the fifth minute and saw his shot saved by Lenny Pidgeley's legs.
The second half opened with a bang with Town's top scorer McGleish grabbing his 13th goal of the season within a minute of the restart. He nipped in ahead of Richard Shaw to collect a right-wing cross by Jason Crowe and beat Pidgeley on his near post.
The second goal arrived with 19 minutes left, and this time McGleish was the provider, as he robbed Shaw and laid a perfect pass into the path of Holt who timed his run into the box well before side-footing a shot past Pidgeley.
Defender Luke Chambers was denied by Pidgeley's brilliant 80th-minute save, the goalkeeper throwing himself to his left to turn away a goalbound header following a free-kick by Eoin Jess.
At the other end Millwall briefly threatened a flicker of a recovery when Bunn turned away a shot by substitute Jody Morris, but Bradley Johnson set the seal on the night with a tremendous last-minute 25-yard shot which skimmed along the turf before going in off a post.