Saints had held a 13-0 lead following a try from lock James Cannon plus two penalties and a conversion from fly-half Stephen Myler.
But tries from hooker Richard Hibbard and replacement Jonathan Spratt, plus seven points from the boot of stand-off Gareth Owen, brought the Welsh side back to take a 17-16 advantage.
However Myler knocked over another penalty 10 minutes from time to seal the win.
The hosts had the first chance to register points in the opening seconds but fly-half Owen, on his 21st birthday, was off target with his penalty attempt, and then followed that up by missing with a long-range effort in the eighth minute before opposite number Myler gave the Saints the lead after a strong Jon Clarke carry had forced a penalty.
Saints soon extended that lead when Ben Foden (pictured) collected a poor clearance kick to breeze round Vaughton before passing inside for lock Cannon to crash over in the corner, Myler adding the touchline conversion for a 10-0 advantage.
Myler then added his second penalty as the visitors took a stranglehold on the game as they forced several turnovers at rucks and denied the hosts quick front-foot ball.
But the Welsh side finally enjoyed some continuity to give the sparse crowd something to cheer as the move ended with hooker Hibbard being the man to profit after a well-controlled driving maul, Owen knocking over the extras to get the hosts back in the game as half-time approached.
The momentum generated by that score saw the Ospreys make an excellent start to the second half and, although Myler slotted another penalty, the hosts began to show the confidence to keep ball in hand and only a knock-on by Phillips prevented him from crossing under the posts after one such passage of play.
Northampton then saw prop Jon Vickers sin-binned for a culmination of several scrum offences and the extra space created by his absence saw the Ospreys finally make their pressure pay.
Full-back Thomas showed good hands to keep the move going and Spratt was on hand to dive over - moments after replacing Vaughton - after the rampaging Filo Tiatia was stopped just short for a converted score.
Northampton were rocking and Myler missed a penalty to add to their nerves before Owen stepped up to add a three-pointer of his own and give the Ospreys the lead for the first time.
But Myler slotted his fourth penalty with 10 minutes left and the hosts were unable to find a score to claim the win despite some fierce late pressure.