But ultimately they deserved at least a point and perhaps should have grabbed all three. Defender Liam Dolman twice missed close-range headers from corners, the first of them before Marc Bridge-Wilkinson curled the ball from a free-kick over the home defensive wall for the 26th minute opener.
But Northampton were level three minutes later. Goalkeeper Keiren Westwood appeared to misjudge a skidding 25-yard drive from Jason Crowe and was beaten on his near post. From that point on, Northampton ran the show and could have led before the break with both Daniel Jones and Johnson firing over.
Carlisle regained the lead against the run of play when Mark Bunn dropped a free-kick under pressure which allowed Joe Garner to slam home his ninth goal of the season and his third in three games. Bunn clearly thought he had been fouled and became one of eight players booked for his protests.
Carlisle threatened to extend their lead when Bunn pushed away an angled drive from Danny Carlton, while substitute Paul Thirlwell saw a rising effort just drift off target. Northampton's passion was just what manager Stuart Gray had asked for following their 3-0 defeat at Swansea on Tuesday and the final ten minutes saw them peppering the visitors' goal.
Westwood needed to be at his most spectacular in the 83rd minute to tip a long-range effort from substitute Ryan Gilligan onto a post, while David Raven headed a Dean Bowditch header off the line. There were four minutes of stoppage time and it was during this finale that Johnson popped up for his fourth goal of the season.