James Constable notched his 98th goal for the club with a powerful low drive from the right edge of the box in the 44th minute, following a fine pass from Andy Whing.
And in the second minute of stoppage time, as half-time loomed, Constable won a penalty, thanks to a positive run that ended with a trip by Ben Tozer.
Danny Rose converted the spot kick with a cool finish into the bottom right-hand corner as Matt Duke dived the other way.
For both Constable and Rose, it was their fourth goals of the campaign.
The Cobblers, struggling near the foot of League Two, squandered good opportunities in the first half, Kevin Amankwaah drove into the side-netting and Darren Carter smashed a 20-yard shot against the post.
Substitute Ivan Toney, denied by a last-ditch block by Michael Raynes, also had a volley saved by goalkeeper Ryan Clarke.
Constable might have put the game further out of Northampton's reach late on, but his side-footed effort drifted wide.