The Cobblers have now suffered only one defeat in ten games, but manager Stuart Gray was left to reflect on two points dropped and a tough schedule ahead with matches against Walsall, Bristol Rovers, Swansea, Nottingham Forest and Carlisle in the next four weeks.
Crewe have now won only once in their last 11 matches and suffered a worrying hamstring injury to Nicky Maynard, which will limit their attacking options in the next month. But manager Steve Holland took heart from an improved defensive display which kept the home club at bay.
Goalkeeper Ben Williams was the visitors' hero with a string of decent saves, beginning in just the second minute when he somehow pushed a 20-yard drive from Ryan Gilligan around the post.
Before he limped off, Maynard saw his goalbound lob cleared by Mark Little and he almost turned in a cross from Kenny Lunt, but his absence handed the Cobblers the initiative.
Williams' best stops saw him keep out a fierce Danny Jackman drive in the final minute of the first half, as well as denying Poul Hubertz in the second half.
Ryan Lowe, whose goal separated the sides at Gresty Road in November, replaced Gary Roberts at half-time and should have scored in the 49th minute only to miss the target from the edge of the box with a clear sight of the posts.
Northampton had all the possession as they tried to cash in, but some resolute defending by Crewe kept them at bay, with Williams having the last word by pushing away a dangerous cross from substitute Jonathan Hayes.