But they had to come from behind to earn the points against a Southend side looking for their third win on the bounce.
New signing Leon McKenzie almost marked his Northampton debut with a goal in the second minute but his shot was deflected wide after Ryan Gilligan's volley was blocked.
Ryan Hall tested Northampton keeper Chris Dunn just before the break and Anthony Grant went close with a 25-yard free-kick shortly after the restart. And it was Grant who broke the deadlock in the 56th minute when he volleyed home a cross from Bilel Mohsni.
But Abdul Osman equalised in the 63rd minute and Holt headed home the winner from Michael Jacobs' corner. Osman went close to grabbing a second in the 84th minute but his header hit the post.
Source: PA
Source: PA