Marcus Smith orchestrated Harlequins' first victory at Franklin's Gardens since December 2012 as Northampton's disastrous home form continued.
Smith set up two tries with precisely-weighted kicks and applied the coup de grace by scoring Quins' sixth try.
Danny Care and Nathan Earle gave Quins control before Mike Brown, Alex Dombrandt and Scott Steele scored.
Tries from Nick Isiekwe, Rory Hutchinson and two from Lewis Ludlam rescued Saints a losing bonus point.
It was Northampton's eighth consecutive home defeat - extending their worst run of the professional era - and they only made the score slightly respectable by exploiting errors with Quins 20 points up.
The visitors dominated the game and, with Smith swiftly directing their attack, kept the ball alive with clever offloads and neat handling - a feature of all their tries - to bounce back well from an opening round 33-3 defeat at home to Exeter.
With a 23-17 lead at the break, Smith's pinpoint kicking helped grow the advantage into an insurmountable one.
His grubber found full-back Brown down the right wing and a penalty soon followed that Quins took quickly from under the posts before Care's delayed pass sent Brown over.
A second Smith kick, this time cross-field to the right wing, was gathered by number eight Dombrandt and he powered his way over for the bonus-point score.
And with the final play of the game, Smith took Andre Esterhuizen's offload and skipped round two defenders to cap off a tremendous afternoon for the Harlequins fly-half.
Northampton Saints: Mallinder; Tuala, Proctor, Francis, Collins; Grayson, Mitchell; Waller (co-capt), Marshall, Hill, Ratuniyarawa, Ribbans, Isiekwe, Ludlam (co-capt), Wood.
Replacements: Fish, Auterac, Franks, Coles, Adendorff, Taylor, Dingwall, Hutchinson.
Harlequins: Brown; Earle, Northmore, Esterhuizen, Murley; Smith, Care; Garcia Botta, Baldwin, Louw, Young, Lewies (capt), Lawday, Evans, Dombrandt.
Replacements: Gray, Els, Kerrod, Tizard, Chisholm, Steele, Lang, Marchant.