The hosts looked set for a fifth win in six after first-half goals by David Worrall and Ryan Lowe. But Courtney Herbert pulled one back in the 66th minute and substitute Adebayo Akinfenwa headed home with 16 minutes left to stretch the Cobblers' unbeaten run to four.
Knill is missing four senior players through injury and did not have a recognised striker to bring on as the Shakers tired in the second half.
"It probably was two points dropped but I thought the performance was excellent from start to finish," he said. "Some of the football we played was the best here for a while. It had pace, energy, and the only thing that was missing was a third goal.
"But just look at their bench and look at mine. We have no squad whatsoever yet we're still competing. Northampton came down last year and were one of the favourites to go up, and we were by far the better team.
"So it was a fantastic effort again by the players and even though it does feel like a loss, for me it's still a point forward. If we continue to play like that there aren't too many teams that can match us."