The Saints nearly blew another large lead after they were held to a draw by Exeter last week having been 33-7 ahead.
Northampton were 24 points clear at 31-7 come half-time at Gloucester's Kingsholm ground, before edging their way to victory despite being without several leading players.
The Saints were in command at the break following tries from flanker Tom Pearson, centre Tom Litchfield, scrum-half Archie McParland and full-back George Hendy, with Anthony Belleau kicking four conversions and a penalty.
But the Cherry and Whites came roaring back in the second half through tries from lock Cam Jordan (two), centre Will Joseph, flanker James Venter and prop Afo Fasogbon, with Ross Byrne kicking five conversions as Saints saw Hendy, Pearson and Tom Lockett all collecting yellow cards.
Northampton were without 19 players - including their four-strong British and Irish Lions contingent - through injuries or unavailability, but two Belleau penalties in the second half ultimately saw them secure victory.
"It was a carbon copy, almost," said Northampton director of rugby Phil Dowson. "We lost momentum and our discipline was very poor, playing with 13 players for large periods of time.
"The first kick-off of the second half, they scored from - more or less - and it is clearly something we need to be better at."
The result left Northampton fourth in the table after two rounds, with Gloucester still looking for their first league win of the season.
"At half-time that was a pretty big scoreline to pull back and we have definitely learned something about players we didn't know before," said Gloucester boss George Skivington.
"It (two points) is better than coming out with nothing but ultimately that first half is a big hill to climb.
"I didn't feel the boys were far off but we must have dropped more ball than we did in half of last season. We are going to see what we are made of now and find out about each other."