Lewis Wilson broke the deadlock five minutes before the break with a goal on his full debut. Toni Silva did well to get in a shot from a tight angle which Paulo Gazzaniga could only parry and Wilson smashed home the rebound.
Earlier, Gillingham went close with Charlie Lee heading over from a Danny Jackman corner, while former Cobbler Jackman also fired over from a good position after good work from Danny Kedwell. But Cobblers went closest in the 24th minute when Michael Jacobs saw his shot tipped on to the post by Gazzaniga and Wilson fired the rebound across the face of goal.
The Gills equalised nine minutes after the restart when Kuffour grabbed his fourth goal of the campaign against Northampton, having completed a hat-trick in the reverse fixture. Kuffour pounced after goalkeeper Neal Kitson failed to deal with a low cross from Kedwell to net from close range.
Looking for the goal to take them to within touching distance of the play-offs, Gillingham got on top and Lewis Montrose should have given them the lead midway through the half but took too long and the chance went begging.
Jackman went close when his free-kick whistled the wrong side of the upright but in between substitute Brett Williams nearly restored Northampton's lead, only to see his header sail over the bar from a Luke Guttridge free-kick.