The home side picked up only their second win of the season, and the first for caretaker manager Ian Sampson, as Moore's men failed to produce a fairytale return for him after his four year absence.
After some early Millers pressure with an unchanged line up from the win over Barnet, it was ironically the home side that took the lead as Ryan Gilligan smashed home an angled drive from 20 yards leaving Andy Warrington with no chance on 11 minutes.
Gilligan was then called into defensive duty when he blocked Danny Harrison's best efforts to equalise, before Nick Fenton headed a corner just wide.
Moore suffered his first injury blow under his second spell in charge as Tom Pope left the field just before the break with injury and was replaced by Ryan Taylor.
But just 40 seconds after the interval the Cobblers made it 2-0 when veteran Steve Guinan set up Courtney Herbert who's shot crashed off the underside of the bar and bounced over the line, as the ball was cleared the referee awarded the goal after consulting with his assistant.
The game was all but over on the hour as Luke Guttridge's drive took a wicked deflection off skipper Ian Sharps to leave Warrington stranded.
The Millers finally got into the game in the final 20 minutes with Warrington still struggling through injury after a 50-50 first half collision.
Nicky Law's near post drive was parried by Dunn and then Adam Le Fondre's deflected effort was tipped over the crossbar.
A consolation did arrive with 12 minutes left as sub Micky Cummins set up Le Fondre who was pulled back in the box as he raced clear, and he converted the spot kick himself - but Rotherham were left to reflect on an evening of disappointment.