Goals from Christopher Missilou and Danny Rose proved to be enough for Northampton to take the points despite a Tyler Smith penalty and a late Town onslaught.
Northampton looked the sharper side early on with Nicky Adams brought down after being clipped by Jonathan Grounds, the resulting set-piece cleared by Akin Odimayo.
The hosts made the breakthrough on eight minutes when Adams mazy run ended in a brilliant stop by Kovar but Christopher Missilou was there to head the rebound into an empty net.
Town had most of their luck in the first-half from the right-hand side with Jordan Stevens causing trouble on a few occasions, but shots from Jack Payne and Matt Smith found Jonathan Mitchell’s gloves relatively easily.
Just over twenty minutes in, Town looked to stretch the Cobblers with Matt Smith finding Jonny Smith, but the winger’s strike was just too high to trouble the ‘keeper.
Town found themselves two-down moments before the half-hour mark, when Danny Rose’s left-footed effort nestled into the corner.
Town looked positive despite the circumstances and came close through Hallam Hope, but the striker’s shot rattled the side-netting.
From the 45th minute, Town looked in the ascendency for the majority if not the entire half.
Jordan Stevens had the first chance after the break when he was slipped in by Hallam Hope but the Stevens’ shot was blocked by a Northampton body.
It was Stevens again who looked sharp when his cross seemed to initially catch out Mitchell but the Cobblers’ keeper was equal to it.
Tyler Smith was brought on with twenty minutes to go and within six minutes, halved the deficit. The Striker was brought down just inside the box and his powerful spot-kick was too much for Mitchell.
Smith then went close again, turning two Northampton defenders but his shot across goal was agonisingly close to levelling the scoring.
A minute into injury-time, Joel Grant looked to have put Town level only for the referee to blow his whistle for what he thought was a foul on Mitchell.
Town head to Oxford on Saturday, looking for a first League win since the end of September.