Jim Mallinder’s men had been 10-6 up at half-time after a fantastic first period, which saw Ken Pisi finish off a fine team try and Stephen Myler slot a penalty and conversion.
But Saints should have had far more to show for their immense efforts, with Myler missing a couple of penalties and Jamie Elliott failing to ground the ball in the corner.
And Saracens improved beyond recognition after the break, taking advantage of tiring Saints.
Chris Ashton’s score against his former club put Sarries in front and Chris Wyles rubbed salt in the wounds late on.
England fly-half Owen Farrell ended the day with 19 points to his name, while Courtney Lawes’ last-gasp try was little consolation for battered and bruised Saints.
The men from Northampton headed to Allianz Park shorn of a host of first-team stars, including Dylan Hartley, Kieran Brookes, Tom Wood and George North.
But they started with real tempo, winning two early penalties from Saracens.
However, on both occasions the lineout faltered, squandering chances to put pressure on the home defence.
At the other end, Saracens took some early points, with Farrell landing a fine kick.
Myler had a great chance to level it up, but he was left disappointed as his effort drifted to the left of the posts.
Saracens were shedding penalties at an alarming rate though and they soon lost Will Fraser to the bin for a late hit on Ben Foden in the air.
But Myler again squandered the opportunity from the tee and Saracens were enjoying constant reprieves, the biggest of which was still to come.
Fine work from Teimana Harrison and Ben Nutley carried Saints into enemy territory and when the ball went wide, Elliott got in at the corner.
But he failed to ground the ball, which wriggled out of his grasp at the vital moment, and Saracens got the chance to get out.
Saints weren’t disheartened though and they soon had the score their play merited.
Myler, Christian Day and Harrison combined superbly to set up Ken Pisi for an easy run to the line.
Myler finally found his kicking boots with a tidy conversion, but Farrell responded with an ambitious attempt from the halfway line.
Fraser returned with his team just a point down and Saints soon saw another lineout wasted in a good position as Lawes was unable to gather cleanly.
Saints were running all over Saracens, winning penalty after penalty, but when they did finally pouch a lineout in the home 22, they were driven out of possession.
But it was all Saints and after Elliott’s scything run from the edge of his own 22, the men in grey won another penalty, which Myler landed to make it 10-6.
Saracens knew they had to up their game significantly after the break and they thought they’d scored within two minutes of the restart as Duncan Taylor went over.
But Saints escaped as Fraser was adjudged to have impeded Luther Burrell in the build-up, with referee Jerome Garces awarding the away side a penalty to allow them to clear their lines.
Saints were soon hit with a big injury blow as impressive skipper Foden was forced off with a groin injury, meaning Harry Mallinder came on at full-back.
And Saracens soon made the most of their increase in territory as Farrell slotted an easy penalty from in front of the posts.
But the Saints response was strong and another kickable penalty was earned, with Myler making the most of it to restore the four-point advantage.
Saracens missed a chance when Alex Goode knocked on at the crucial moment, but they soon had a penalty as they got a big shove on at a Saints scrum.
Farrell landed it to again cut the gap to one point and Saints quickly opted to introduce experienced lock Victor Matfield and prop Campese Ma’afu.
The away side were showing fatigue and Ashton flew over, performing the ‘Ash Splash’ as he scored.
Farrell added the extras and Saracens were now leading, enjoying a six-point advantage with 10 minutes to go.
And it was to get worse for Saints before the end as JJ Hanrahan’s pass only found Wyles, who gleefully pounced and scored.
Farrell again converted before Lawes went over in the corner to register a late consolation for Saints.
Myler converted but it was to be the final kick of his side’s Champions Cup campaign.
Saracens: Goode; Ashton, Taylor, Barritt (c), Wyles; Farrell, Wigglesworth (De Kock 40); M Vunipola, Brits (Saunders 78), Du Plessis; Itoje, Kruis; Wray (Rhodes 52), Fraser, B Vunipola.
Saints: Foden (c) (Mallinder 47); K Pisi, G Pisi (Hanrahan 70), Burrell, Elliott; Myler, Fotuali’i (Kessell 75); A Waller (Ma’afu 61), Haywood (Marshall 78), Hill (Denman 75); Craig, Day (Matfield 61); Lawes, Nutley, Harrison (Paterson 75).
Referee: Jerome Garces (France)