After taking an early lead, they were close to seeing it vanish in the second half but this was a game where winning was everything.
The City manager admitted his club were close to crisis after a dispiriting midweek Johnstone's Paint Trophy defeat by rivals Bristol Rovers.
He made four changes, reshaped to play with three central defenders and sent the team out with a shoot on sight policy.
It all began when Kevin Betsy - a £150,000 recruit from Wycombe in January - neatly slipped Andy Holt down the right to set up a volley for Steve Brooker.
A couple of shots apiece from David Noble and Brian Wilson then signalled the Cobblers defence was in for a testing afternoon.
Mark Hughes was diving in with one tackle after another to beat back the home attacks but the only goal when it came followed hard on the Cobblers' best chance of the day - a glancing header from Kenny Deuchar at a corner.
From the goal-kick, Noble, who is still seeking to re-establish himself as a City regular, led a fast breakout which saw Brooker driving a half-volley at Mark Burn. The keeper parried it with one hand but the ball ran out to Betsy who promptly knocked it back past him.
With his pace and control on the right, Betsy gave City a fresh dimension as a wing-back who gradually gave up their defensive side of the job.
But there should still have been a goal for Northampton when Louis Carey gave away a free-kick on the left.
It was swung in by Bradley Johnson but, with the home defence bare, experienced midfielder Ian Taylor missed his header.
A frenetic first half gave way to a tactical exercise in the second. Northampton worked out a way to give Sam Aiston a role after he had been snuffed out earlier by Cole Skuse.
The link-up man became more influential and forced City to counter by falling back on a more familiar back line of four.
City's lead was far from secure, but as they looked for a second goal Wilson found himself booked for celebrating a goal that never was.
When he ran in a cross from Noble he whipped off his shirt to signify his delight, but it was all so unnecessary as the offside flag was already up.