The home side's cause was aided by Northampton being reduced to 13 men by the sin-binning of Ben Foden and Dylan Hartley.
The departure of replacement scrum-half Foden allowed the home side to exploit their advantage as Kevin Sorrell and Glen Jackson combined to send Penney over in the right corner in the 66th minute.
Six minutes later England squad hooker Hartley followed for a similar offence of killing the ball in front of the posts. Again, Saracens opted for the scrum and close-season signing Owen drove over the line from close range. Fly-half Jackson converted both tries to finish with 13 points, after making up for two early misses by landing three subsequent penalties, and his replacement Gordon Ross completed the scoring with his late penalty.
Northampton had originally announced an unchanged line-up but suffered a double blow before the kick-off. After deciding last night to leave out Irish international flanker Neil Best, who could face a lengthy ban when he appears before an RFU disciplinary panel on Tuesday, Saints then lost right-wing Chris Ashton with a tooth abscess.
Chris Myler came in at full-back with skipper Bruce Reihana switching to the right-wing while Mark Hopley replaced Best in the back row. Northampton were in front until Penney struck. The visitors were indebted to the accurate kicking of full-back Myler, who landed three penalties and a superbly-struck drop goal from near the halfway line.
Northampton decided it was ''not appropriate'' to play Best ahead of the hearing after he was cited for ''illegally making contact with the eye or eye area'' of Wasps star James Haskell during last weekend's 24-20 victory over champions Wasps.
If found guilty, the suspension range for that category of offence varies from six weeks to two years. Events went from bad to worse for the visitors when centre James Downey limped off after only 12 minutes to be replaced by Chris Mayor.
Before Downey departed, only two uncharacteristic penalty misses by Jackson prevented Saracens from going ahead. Adam Powell, Jackson, Penney and Richard Haughton combined to produce one dazzling early move for Saracens but over-elaboration in attack proved their undoing and Saints gradually worked their way into the game.
They took the lead with a 24th-minute penalty from Myler after scrum-half Lee Dickson was prevented from clearing the ball from a ruck. But Jackson levelled the scores seven minutes later, succeeding at the third attempt from just inside the Northampton half.
Northampton moved back in front with Myler's second penalty after Saracens were caught offside in front of their own posts in the 38th minute, before being denied the first try of the match on the stroke of half-time when Dickson's pass which released replacement Mayor on a clear run to the line was ruled forward.
Myler struck again five minutes into the second half with a penalty from wide out on the left near the halfway line, and his side had another try ruled out because Sean Lamont had knocked on before Spencer went over. But it all counted for nothing as Saracens stepped up the pressure in the second half to clinch their second home victory in a week, after hammering Newcastle 44-14 last Sunday.
Saracens 26 (3) Tries: Penney, Owen Pens: Jackson (3), Ross Cons: Jackson (2)
Northampton 12 (6) Pens: Myler (3) DG: Myler
Saracens: Haughton, Penney, Sorrell, Powell, Ratuvou, Jackson, de Kock, Aguero, Ongaro, Johnson, Borthwick, Vyvyan, Jack, Saull, Owen. Replacements: Cairns, Visagie, Chesney, Skirving, Rauluni, Ross, Wyles.
Northampton: Myler, Reihana, Ansbro, Downey, Lamont, Spencer, Dickson, Tonga'uiha, Hartley, Murray, Fernandez Lobbe, Day, Hopley, S. Gray, Wilson. Replacements: Shields, Stewart, Smith, Rae, Lewitt, Foden, Mayor.
Referee: Martin Fox (RFU)