Kidderminster moved six points clear of the relegation zone thanks to well-taken goals from Dean Keates and Dean Bennett.
Chris Hargreaves pulled a goal back for Northampton but it was not enough to stop Jan Molby's men from securing their first league 'double' of the season.
Defeat dented the Cobblers' play-off hopes, which had been boosted by five victories in their previous six outings.
A delighted Molby said: "I thought the win was deserved. The result apart, I thought at times we played some excellent football.
"But the most pleasing thing is that when they scored to make it 2-1, instead of allowing them to get on top, we really took the game back to them." Harriers had the majority of possession throughout an entertaining match and were worth their 1-0 half time lead.
The breakthrough came in the 29th minute when a deflected cross from Ian Foster broke to Keates who hammered in a fiercely struck drive from 22 yards.
It was the midfielder's first goal in five appearances following his move from Hull City.
A couple of minutes later, Bennett had a cross-shot flash wide before John Williams was denied by a timely tackle from Ian Sampson on the stroke of half-time.
The Cobblers failed to get in an on-target shot during the opening period although Martin Smith did his best with a powerful drive from the edge of the box in the 19th minute.
The entertainment level remained high in the second half, which was only two minutes old when Bennett scored with a first-time volley from just inside the area following a pinpoint cross from Foster.
Battling Northampton pulled a goal back in the 56th minute when Hargreaves was allowed to head in from close range after a corner from Smith.
Keeper Lee Harper was the visitors' hero in the 69th minute when he managed to push a lobbed shot from Bennett onto the bar before the danger was cleared.
Northampton boss Colin Calderwood said: "We got what we deserved which was nothing.
"At the minute, away from home we are not good enough to grind out a result."