The home side, who had previously failed to score in three of their last four home league games, took the lead on 23 minutes when Matty Blair flicked the ball around Town defender John Johnson before calmly slotting the ball past Town keeper Lee Nicholls after a good long ball from Ashley Chambers.
Things then got worse for the away side when they were reduced to 10 men on 38 minutes when Johnson was shown a straight red card for a wild challenge on York's Chris Smith.
Northampton started the second half well, and scored a deserved equaliser when Chris Hackett's free kick was spilled by York keeper Michael Ingham, allowing Adebayo Akinfenwa a simple tap-in from close range.
Both sides pushed for a winner late on with Blair hitting the woodwork, and Danny East wasting a good chance for Northampton but no winner could be found.
