Manager Alex McLeish decided to start with a side made up with those players not selected in his starting XI for the friendly match against Derby County at Pride Park on Saturday.
James McFadden came close to opening the scoring on 20 minutes but his well-struck free-kick from the edge of the area came back off the upright.
Just two minutes later the Cobblers took the lead. Maik Taylor's goalkick was headed back into the Blues half where it found Billy McKay who beat the Blues keeper with ease from close range.
Jordan Mutch came close to equalising for Blues right on the stroke of half time but his long range effort rattled the top of Cobblers crossbar.
Five minutes into the second half Blues did draw level when a superb 25-yard half-volleyed effort from Cameron Jerome flew past a helpless Paul Walker in the Cobblers goal.
Mcfadden then gave Blues a 2-1 lead on 69 minutes after some neat build-up play but substitute Liam Davis equalised for the hosts with just five minutes of the match remaining.
Northampton: Walker, Johnson, Beckwith, Holt (Harris, 71), Hall, Rodgers (Wedderburn, 52), Gilligan (Herbert, 71), Osman, Thornton (Davis, 52), Purcell (Guinan, 52), McKay (Jacobs, 52). Subs not used: Gherasim, Slowe, Konstantinou.
Blues: Taylor, Carr, Ridgewell, Kerr, Mutch, Michel, Bowyer, Valles, McFadden (Murphy, 74), Phillips, Jerome. Subs not used: Foster, Parnaby, Johnson, Dann, Larsson, Gardner, Ferguson, Fahey, O'Connor, Zigic.
Referee: Dean Whitestone
Blues' next pre-season friendly fixture is an away game against MK Dons on Tuesday night.