Matty Blair put the hosts in front with a cool finish after a long ball forward from Ashley Chambers.
Despite Louis Moult's sending-off late in the first half, the Cobblers started the second half well and scored a deserved equaliser when Chris Hackett's free-kick was spilled by York goalkeeper Michael Ingham, allowing Adebayo Akinfenwa a simple tap-in from close range.
Mills said: "We started the second half very poorly. We we're very sloppy in the opening 10 minutes, which gave them a lift and then they went and got the goal. That gave them another lift and we just couldn't get going in the second half.
"But we have got ourselves another point and it is important we come out on Saturday (at home to AFC Wimbledon) and go and get the three points."
Speaking about Blair's goal, Mills added: "We all know what he is capable of. That is why I play him in the middle. He has come from that middle position again and has gone around the defender superbly. Once he has gone around him it is never easy to score and he has put it away really well."