Haughton took the man-of-the-match award but made the starting line-up for the match only because original right-wing choice Paul Bailey was stuck in traffic on the M25.
He took his unexpected opportunity with the opening try in the 10th minute and then weaved his way through the Northampton defence in the 73rd to strike the killer blow.
Bailey finally made it to Vicarage Road in time to replace injured fullback Dan Scarbrough just before half-time – but Haughton served notice that he intends to reclaim his number 14 shirt on a regular basis.
He scored the first try, going over in the right-hand corner to finish off a fine move set up by centre Thomas Castaignède and fly-half Mark Bartholomeusz – and his second touchdown was an even better effort.
In between, prop Ben Broster forced his way over from close range following a 43rd-minute line-out.
Castaignède added a penalty and converted Haughton's second try before left-wing Ben Johnston had the final say with a drop goal deep into injury time.
Remarkably, Northampton could not manage a try despite having a big pull in possession and territorial advantage.
They were twice denied by the fourth official, who studied video replays before ruling that forwards Matt Lord and Andrew Blowers had failed to ground the ball after driving in from close range.
With both sides determined to turn the tide of defeat, there was an air of anxiety which led to errors – frequently interrupting the flow of play as Northampton plunged to their fourth successive league defeat.
Even the introduction of out-of-favour England World Cup-winning left-wing Ben Cohen from the bench at half-time failed to find a way through.
Cohen had little chance to show his finishing power.
He was totally unmarked when the Saints squandered a four-on-one attacking opportunity as England hooker Steve Thompson hung on to the ball too long before throwing out a high pass to fly-half Shane Drahm, who promptly dropped the ball.
Then when Saints again had the numerical advantage Cohen tried to go it alone and was ushered into touch.
Northampton were left with just two penalties each from Drahm and fullback Bruce Reihana to show for their efforts – and after winning their opening two matches, they are drifting towards the relegation zone.
For Saracens:Tries: Broster, Haughton 2 Cons: Castaignède Pens: Castaignède Drop: Johnston
For Northampton Saints:Pens: Drahm 2, Reihana 2