Jamie Forrester and Marco Gabbiadini combined to send Luton home empty handed and end their unbeaten seven-match league run.
The contest had been built up around the return of former Cobblers striker Steve Howard, but Luton's top scorer endured a fruitless afternoon while Forrester n particular continued his recent good form.
Forrester took his seasonal total to six, five of them in the last fortnight as Northampton took a stern grip of the contest in the first 20 minutes.
He firstly tucked home a pass from Paul Harsley and then stretched a leg to divert a first- time Gabbiadini cross pass Cedric Berthelin.
Northampton could of extended their lead but Derek Asamoah hurried a 34th minute chance when through on goal.
At the other end, Tony Thorpe had a goal disallowed and the same player was denied by the outstretched leg of Lee Harper when he ran on to a Howard flick-on.
Luton began the second half with greater menace and Ian Sampson was forced to make a headed clearance just yards from goal but the home side virtually sealed the points with an exquisite piece of finishing by the veteran Gabbiadini, to cap an outstanding performance.
He latched on to a crossfield pass by Forrester and spotted Berthelin off his line, sending in a pin-point lob from 35 yards which went in under the crossbar.
Luton had chances to claw their way back, but Howard headed over a Sol Davis cross and sub Peter Holmes sent another header wide from a good position.
Northampton's assistant manager Martin Wilkinson said: "Although we were beaten 4-0 at Oldham on Tuesday, we turned in the type of performance which restored the players belief and this result was some reward for that."