With England boss Stuart Lancaster watching in the stands, the persistent rain made it an attritional game as Nick Evans kicked all of Quins' points, with his ninth penalty being the last kick of the game to deny Northampton a losing bonus point.
Quins had the edge up front, with Northampton's lineout malfunctioning and in Mike Brown, the visitors had the safest hands on the pitch as he took every up-and-under launched at him.
Northampton's points came through two penalties from Stephen Myler and one from Ryan Lamb.
But they will be ruing a first-half Ben Foden try being ruled out for a forward pass, which replays showed was wrongly called by the touch judge.
Harlequins' front row asserted their extra muscle early on, driving Northampton back 10 metres at the first scrum to earn a penalty, which Evans slotted to give the champions a fourth-minute lead.
Quins were winning the early territory battle on a surprisingly good pitch considering all the rain, but Evans missed his second kick. Myler made him pay immediately afterwards by evening up the scores.
Foden thought he had scored the opening try of the game but the touch judge ruled George Pisi's slap pass to the full-back was forward.
Replays on the big screen seemed to show it was not and the home crowd let their disapproval be known. Referee Wayne Barnes did not go to the TMO either as he had already stopped following the play.
To compound Saints' misery Myler missed a straight forward penalty soon after and Evans added three points from a similar position to make it 6-3 after 29 minutes. Three minutes later Saints turned down a shot at the posts from 40m and kicked to the corner only to see the attack come to nothing.
Six minutes before half-time, Saints kicked another gettable penalty to the corner only to see George Robson steal the lineout.
With incessant rain making handling problematic a tremendous catch under pressure from Brown allowed Nick Easter to sprint from one 22 to another only for wing Jamie Elliott to gather his chip over the last tackler and a penalty ended the promising Quins break.
A 15m break from James Johnston forced a silly penalty out of Paul Doran Jones, but Evans saw his kick slide wide.
Quins were keeping the game in Saints' half, but with 25 minutes to go prop James Johnston was sin-binned trying to kill a Saints break by lying on the ball on halfway.
Soane Tonga'uiha had turned the ball over in his 22 to inspire the break. Joe Marler was lucky not to get another yellow when he killed the ball in his 22. Saints this time decided to kick for the posts and Myler made it 6-6.
Despite having the extra man the home side made little impression and two Foden errors cost them dear.
First, the England back dallied fielding a kick and was penalised for holding on to allow Evans to put Quins back into the lead.
The 27-year-old then spilled an up-and-under and a fifth penalty from Evans with seven minutes to go saw the home fans start to spill out of the ground.
Ryan Lamb came on to add a penalty as Saints decided against going for a try five metres from the line, but Evans denied them even a point.
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