Andy Symons scored twice but Saints were eventually made to suffer by Saracens as their winless start to the season continued at Franklin's Gardens.
The black, green and gold were ahead on numerous occasions but they were beaten 54-28 by their familiar foes from Allianz Park.
Saints were only 23-21 down at half-time, with Tom Whiteley's last-gasp penalty giving Saracens the lead.
But Mark McCall's men pulled away during the second period before their replacement back, Charlie Watson, was red carded for kicking Symons in the head.
Symons, who was on the ground at the time, was also punished, receiving a yellow card for holding on to Watson's foot in the build-up.
It was a late flashpoint in a frenetic encounter, in which the lead changed hands nine times overall.
But it didn't alter the outcome of the match as Saints were left to rue a third defeat in as many games this season.
They are now unable to qualify from their Premiership Rugby Cup pool, with just one group game, at Leicester Tigers next Saturday, remaining.
Holders Saints had headed into the clash with Saracens on the back of an eventful defeat to Wasps, and they had to endure some early pressure.
Saracens intercepted close to halfway, and they almost scored on two occasions, only to waste big chances.
The second saw Alex Lozowski looking certain to dot down, but he knocked on under pressure from former team-mate Henry Taylor.
But it wasn't long before Saracens made the pressure pay as fast hands from Alex Lewington released full-back Matt Gallagher, who cruised in out wide.
Scrum-half Whiteley missed the conversion and Saints responded well, with Taylor continuing his sharp start and Ryan Olowofela's fast footwork causing Saracens problems.
Symons powered over under the posts to give Saints reward for their efforts, and James Grayson converted to earn his side a 7-5 advantage.
But Whiteley immediately restored Saracens' lead after Saints were penalised for offside.
Taylor was running the show for Saints though, with everything he touched turning to gold, and he claimed a richly deserved score after picking up from a scrum and darting over.
Grayson converted to make it 14-8 and Saints had their tails up, with Saracens submerged in their own half.
But after a lengthy stoppage following an unfortunate injury for Saracens flanker Sean Reffell, Saints let the away side slip through their grasp.
And winger Rotimi Segun made his old club pay as he finished in style in the corner.
Whiteley again failed with the conversion in slightly windy conditions, but he made amends with a much better soon after as Saracens scored again through Nick Tompkins.
The period of inactivity during Reffell's injury had disrupted Saints' momentum, and they desperately needed to rediscover it with five minutes to go until the break.
They did just that as Taylor again played his part before another of the better performers in the first period, Symons, did the rest with some tidy footwork.
Grayson converted to put Saints back in front at 21-20 up, but Whiteley had the final say of the half as he kicked a penalty given for a high tackle from Mitch Eadie.
And Whiteley was on target again early in the second half as JJ Tonks was penalised at the breakdown.
Saints steadied themselves and almost scored soon after as Olowofela hunted down a Rory Hutchinson kick ahead, but Gallagher did well to get there first and prevent the try.
But Saints held their nerve and with everything revolving around the awareness and speed of Taylor's play, they scored as David Ribbans latched on to a pass from the scrum-half.
Grayson converted to make it 28-26 in the home side's favour, but yet again Saracens responded.
Segun did some slick work down the right and Ben Spencer, just on for Whiteley, finished the job, also kicking the conversion.
There was plenty and huff and puff after that, but finally Saracens secured some breathing space, which had previously been so rare in a game of fine margins.
Tompkins was the man to provide it as he added his second try of the game, and Manu Vunipola added the kick from the touchline.
At 40-28 down with just 15 minutes remaining, Saints needed to summon one big final shove.
But it was Saracens who scored again soon after as Vunipola did superbly to slalom his way through the Saints defence.
Vunipola was congratulated on his effort by almost all of his team-mates before landing the conversion to make it 47-28.
There was then a real flashpoint as Saracens replacement Watson was red carded for kicking Symons in the head after the Saints centre had held on to his ankle at a breakdown.
Boos rang out as Symons was yellow carded for his part in the incident, meaning Saints would not have a man advantage until the final two minutes of the match.
And Saracens kept coming forward, with Tompkins completing his hat-trick as Saracens yet again hit a half-century of points at the Gardens.
Vunipola converted amid a backdrop of fans flooding out of the ground.
Symons finally returned from the bin, but it was too late as Saracens celebrated a big success.
Saints: Hutchinson (Mathews 56); Olowofela (Bird-Tulloch 54), Dingwall, Symons, Collins; Grayson, Taylor (Tupai 68); van Wyk (Waller 56), van Vuuren (Ma'asi 63), Painter (Garside 64); Ribbans, Moon (Bean 63); Tonks (Brüssow 61), Harrison (c), Eadie.
Saracens: Gallagher (Watson 63); Segun, Lozowski, Tompkins, Lewington (Obatoyinbo 10); Vunipola, Whiteley (Spencer 51); Barrington (Crean 61), Woolstencroft (Pifeleti 63), Ibuanokpe (Wainwright 57); Skelton (Kpoku 61), Hunter-Hill; Christie, Reffell (Isiekwe 28), Wray.
Referee: Craig Maxwell-Keys