Rushden started brightly and they took the lead on six minutes when Peter Hawkins found Drewe Broughton, whose persistence lead to the ball falling back to Hawkins and he drilled home from ten yards out.
Northampton retaliated in the 11th minute when Scott McGleish had a shot well saved by Scott Shearer on 22 minutes, while Rushden full-back Sean Connelly was inches wide with a 20-yard drive.
On 28 minutes McGleish was again in the thick of the action when he saw his header rebound off the post following Martin Smith's free-kick.
On 33 minutes David Bell's cross from the right was almost headed home by Rob Gier.
Northampton fought their way back into the game towards the end of the half and they got somewhat a fortunate equaliser. Scott Shearer dropped Smith's shot over the line and the Cobblers man followed up to make sure.
Northampton came out in the second half looking a far better side and they went ahead on 51 minutes when debutante striker Andy Kirk headed home following a cross by Joshua Low.
Rushden equalised on 56th minutes when Christopher Willmott was adjudged to have fouled Billy Sharp and Brown coolly converted the penalty.
With both sides striving for a winner the game flowed from end to end and only a saving tackle by Hawkins on McGleish in the 77th minute kept the home side level.
In the closing stages Northampton look more likely to score and only stout defending by Rushden kept them at bay.
However there was a dramatic finish when defender Luke Chambers made an error to allow in Sharp and he raced on to shoot past Lee Harper.