Chester showed both sides of their character as they frustrated the home side in a bad tempered battle at Sixfields.
Ian Rush's side played the last 62 minutes with ten men after the dismissal of striker Cortez Bell for kicking home defender Pedj Bojic.
With Chester, who already boasted the division's worst disciplinary record, also having five players yellow carded - four of them in the first half - it looked certain that the Cobblers would cash in on their numerical advantage and continue to make inroads on the league leaders.
It was already 1-1 when Bell was given his marching orders by referee Mike Thorpe.
The home side went ahead in the sixth minute when Julian Alsop, making his first league start the Cobblers, won a header from a David Rowson free-kick and when Chester failed to clear their lines, Martin Smith drilled home a right-foot shot on the turn.
Chester only managed two attempts on goal in the entire match, but one of them saw Town goalkeeper Lee Harper beaten in the 26th minute.
It came from a terrific 35-yard free-kick by Kevin Ellison, but Harper will be disappointed that he was beat inside his left hand post.
City were in danger of completely losing their shape and discipline in the first half, but by reaching the interval on level terms they were able to reorganise, sending on central defender Richard Hope for Sean Hessey, and their habit of conceding numerous free kicks reduced dramatically.
Northampton tried the patient approach to try to break down the visitors and created a handful of chances that should have reaped the extra points.
Scott McGleish was set clear by Smith's raking pass in the 62nd minute but his shot was beaten away by Chris MacKenzie.
Alsop had two clear headers, but both were directed too close to MacKenzie to cause a major problem.
McGleish and Lee Williamson both fired wide of the target, before the Cobblers missed a gilt-edged chance nine minutes from time.
From a Smith corner, the ball went all the way to the back post but Chris Wilmott's free header flew back across goal and wide, when it seemed easier to hit the target.