The Cobblers' former Boston striker Andy Kirk was on target in this fixture for the second season running, but this time around this 22nd minute opener was for the home side when he hooked the ball in from six yards after a fierce drive by Pedj Bojic was blocked on the line.
The visitors rarely looked a threat but still managed to draw level five minutes before the break when Ian Ross drifted in a free-kick towards the near post and Alan White knocked his second goal in three days with a flick header which eluded Lee Harper.
Northampton responded sharply and were in front again before the break.
A long throw by David Hunt reached the penalty spot and former Aston Villa and Derby midfielder Ian Taylor planted a firm header into the top corner to register his first goal for the club he joined in the summer.
The second half took a long time to muster any excitement, although Jason Lee directed a header goalwards from a long up-and-under by Lee Canoville but the effort lacked serious venom and Harper was able to make a comfortable save.
Northampton introduced strikers Eric Sabin and Lawrie Dudfield into the fray and Sabin had a header saved while Taylor also went close with a volley from an Eoin Jess cross with Nathan Abbey diving smartly to save.
The home side appeared to have wrapped up the points seven minutes from time when Jason Crowe registered a first goal for his new club by ramming home a left-foot shot after a pass by Jess.
But Northampton made sure the final moments were nervy ones by instantly conceding at the other end with Ross firing home a low shot from 15 yards after lax defending.