Ronnie Moore's first game back in the dugout ended in defeat at Sixfields after Northampton ended the Millers' seven game unbeaten league run, winning 3-1.
A first half goal by Ryan Gilligan was added to in the second half by a Courtney Herbert strike and an Ian Sharps own goal, with the Millers responding late on with an Adam Le Fondre penalty.
The Millers did look like the better side in the initial exchanges and after a slow opening five minutes they created the first chance of the game.Good interplay between Dale Tonge and Nicky Law allowed the full-back to dig out a cross to the far post, only to see Kevin Ellison nod inches wide with the 'keeper beaten.
Northampton took the lead with their first effort of the game on 10 minutes.After the Millers failed to clear a throw from the right hand side the ball fell to Gilligan, whose right-footed shot arrowed into the top corner from 25 yards.
The visitors came close to equalising five minutes later.A corner from the left was nodded to Danny Harrison on the edge of the penalty area.The midfielder's left-footed shot looked destined for the bottom corner, but goalscorer Gilligan managed to block the effort.
Another Rotherham corner then created another half chance for the visitors.Law swung the cross in from the right, but Tom Pope and Nick Fenton seemed to get in each other's way, with the result being a scuffed header wide of the post.
After a scrappy spell the Millers created a half chance on 38 minutes. Fenton nodded down to Pope, who controlled well with his back to goal before seeing his bicycle kick saved on the line by Chris Dunn.
An injury sustained by Pope whilst defending a set piece prevented him from finishing the first half and he was replaced by Ryan Taylor on 43 minutes.
Northampton Town 1v 0 Rotherham United
The Millers got off to the worst possible start to the second half and allowed the Cobblers in for a second goal. Steve Guinan played in Herbert who crashed his shot from just inside the area against the bar and over the line to leave Warrington well beaten.
Worse was to follow for the Millers in the 59th minute when Northampton added a third. Luke Guttridge smashed a shot towards goal from 20 yards out which cannoned off the unfortunate Ian Sharps who diverted the ball beyond Warrington and into the top corner.
It could have been four two minutes later when the lively Ben Marshall cut in from the right wing before hammering a low shot which whizzed just past Warrington's far post.
Law tested Dunn in 65th minute after neat build up play involving Le Fondre but his shot from a tight angle was comfortably dealt with at the near post.
A minute later and the Millers almost found a way back into the game. Ellison laid the ball into the path of Le Fondre whose shot took a wicked deflection that left Dunn back-peddling but the Cobblers' stopper stretched out a hand to turn the ball over the bar.
Another chance went begging for the Millers in the 71st minute. A Law corner found its way through to the on-rushing Sharps but his shot on the run was stabbed wide of the upright.
With 12 minutes remaining sub Micky Cummins played Le Fondre through on goal but the striker was felled just inside the area by Andy Holt who conceded a penalty but escaped with a booking. Le Fondre picked himself off the ground to drill the spot kick straight down the middle to beat the diving Dunn and reduce the Millers' arrears.
Northampton Town 3 v 1 Rotherham United
Northampton Town: Dunn; Johnson, Guttridge, Hinton, Beckwith (McCready 75), Marshall, Guinan (Akinfenwa 82), Holt, Gilligan, Curtis, Herbert (McKay 52).
Subs not used: Osman, Dyer, Harris, Brown.
Rotherham United: Warrington, Tonge, Green, Fenton, Sharps, Mills (Cummins 67), Harrison, Law, Ellison, Pope (R. Taylor 43), Le Fondre.
Subs not used: Joseph, Lynch, Warne, Liddell, Annerson.