City found themselves trailing at the break thanks to Alex Revell's opener for Northampton but, aided by the half time substitutions of Mark Marshall and James Hanson, McCall's men roared back to completely boss the second half in a one-way period.
The purposeful Marshall fired City level midway into the second period when he crashed home a fierce angled drive from inside the box.
Marshall then turned provider with just four minutes of normal time remaining, his low cross into the six yard box being converted from close range by Jordy Hiwula for the striker's seventh goal of the season.
Reflecting on the game, McCall added: "We started with a diamond shape in midfield today (Saturday) because of Fil (Morais) being out injured and Marshy (Marshall) having a knock from Saturday (vs Bury).
"We had plenty of possession in the first period without really threatening their goal, so we had to change it at half time.
"With James Hanson and Marshy on the bench, we always knew we could throw them on to give us that extra attacking impetus.
"We knew we'd be attacking to our end, over 1,000 City supporters, in the second half and we told the lads to come back in after the game with no regrets.
"We didn't want another draw, we only wanted that win.
"From minute one after the break, we got crosses into the box, we worked their 'keeper and defence, and we put them under real pressure.
"You could see the desire from the lads, they just wanted to go again and get another goal once we'd got the equaliser.
"Marshy knows he can score goals like that, he has tremendous ability with both feet, and I'm delighted for Jordy (Hiwula) as well.
"His movement is great and he keeps getting himself into the right positions.
"I've probably never been involved in a match before where the away side has had such dominance in a half like we had in that second period.
"It would have been an absolute travesty if we'd not got the three points so it is a huge relief that we've got this win.
"This is a good start for the new year for us and a great way for us to reward our travelling supporters.
"Hopefully we can now kick on and take this boost into our home game (vs Chesterfield) on Saturday."