Both sides were short on ideas and lacked any urgency, making a draw a fair result.
Ryan Lowe had come within a whisker of giving Chester the lead inside four minutes as his snap shot crept just past the post, but after that there was little of note.
The visitors' first effort on goal did not come until the 18th minute when Martin Smith put a left-foot effort which keeper Chris McKenzie claimed at the second attempt.
Both sides seemed to be playing within themselves with a slow tempo the order of things particularly in the first half. The one bright moment saw a clever back heel from Lowe send Marcus Richardson away, but his effort was saved by keeper Lee Harper.
The second period saw greater urgency from the home side, with Ben Davies at the heart of everything that Chester were creating.
Northampton boss Colin Calderwood made a double substitution on the hour mark, with Andy Kirk and David Hunt coming on in place of Junior Mendes and Eoin Jess, as he looked to inject some life into his side.
But it was Chester who looked the most likely, and they should have done better with a swift break upfield by Davies being wasted by a poor cross from Lowe.
Seven minutes from time a foul by Luke Chambers on Michael Branch earned the defender a caution and gave Chester a good opportunity on the edge of the box, but Lowe's effort was saved by Harper.
The best chance of the game did not come until two minutes from time when Chris Doig swivelled on a loose ball inside the box, but shot over with the goal at his mercy, leaving the game ending in stalemate.