Harlequins went top of the fledgling Premiership table thanks to another superb kicking performance by former New Zealand fly-half Nick Evans.
Evans, who booted over 16 points from six attempts at The Stoop, has now landed 13 consecutive kicks in two games in his fine start to the season.
Second-half tries from Joe Gray and Ugo Monye also helped Harlequins to their second straight win.
Northampton full-back Greig Tonks ran in his side's only try.
Despite losing openside flanker Will Skinner shortly before kick-off - he complained of a dizzy spell having suffered a head injury last weekend - the hosts struck first when Evans stroked over a fourth-minute penalty.
Evans than extended their lead in the 20th minute with another penalty for offside. Yet, three minutes later, Northampton were ahead, Tonks smashing through two tackles to score from close-range on the right.
Stephen Myler converted to make it 7-6 but the lead lasted only six minutes before Saints went offside again and the deadly Evans, who kicked 19 points against London Irish last Saturday, nudged his team back in front.
You win nothing this time of the season. Victory is a building-block
Harlequins coach Conor O'Shea
Another Evans penalty earned Quins a 12-7 half-time lead - and that advantage was extended just six minutes into ths second half when Karl Dickson broke off the back of a scrum, dummied one challenge and armed hooker Gray to power through by the posts, Evans adding the conversion.
Myler kicked a goal to halt the scoreboard run, but the relief was temporary as Quins scored their second try off a move that had fans out of their seats.
Sublime back-play seemed doomed to failure confronted by a solid defence - but Evans and Jordan Turner-Hall executed a lovely loop-switch that released Monye to score on the left.
The one area where Saints were dominant was the scrum and they won another penalty for Quins collapsing, Ryan Lamb adding the three points to complete the scoring.
Instead of taking control with a substantial lead, Quins began to display serious jitters and it got worse when James Johnson was sin-binned six minutes from time for going off his feet to halt a Saints drive.
But Quins managed to shut out a side who failed to turn huge possession in the final quarter into points.
POST-MATCH VERDICTS
Harlequins director of rugby Conor O'Shea:
"I am delighted to go into the weekend top of the Premiership. But you win nothing this time of the season. Victory is a building-block. The players see all their hard work from pre-season rewarded and confidence grows as a result.
"I was happier than I felt after last week's win at Twickenham because I stressed the importance of upping the tempo of our game, and the players delivered.
"We lost a grip on our set-piece later in the game, but our defence stood firm in the face of some very intense pressure. We expected a physical battle and got one. We met it head on and, I believe, played with more adventure over the 80 minutes."
Northampton Saints director of rugby Jim Mallinder told BBC Radio Northampton: "It was very disappointing. It was always going to be difficult coming here, but we made far too many mistakes in attack and defence.
"They put us under pressure and we didn't play very well. You've got to be philosophical, but we've got lots of lessons to be learnt.
"Quins are tough and they've only got three or four players out. We've got to put this behind us and beat London Irish next week."
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