Centre Mark Tucker scored an injury-time try to give his side a four-try bonus point after Harlequins bounced back from a 24-9 deficit to threaten the visitors' supremacy, but in the end the visitors booked a place in next season's Heineken Cup without too much trouble.
Saints had built their lead around a first-half penalty try, and the conversion from Paul Grayson, second-half tries from prop Brett Sturgess and Nick Beal, both converted by scrum-half Matt Dawson, and one Grayson penalty.
But NEC Harlequins refused to back down, with a late penalty try, to go with three first-half penalties from Irishman Paul Burke as well as the conversion and a drop-goal from the latter, putting them within striking distance at 24-19.
The visitors, however, retained their composure, with midfielder Tucker crossing late in the game to seal the win and the bonus point, whilst taking away 'Quins' bonus point for finishing within seven points.
For NEC Harlequins:Try: PenaltyCon: BurkePens: Burke 3DG: Burke
For Northampton Saints:Tries: Penalty, Sturgess, Beal, TuckerCons: Grayson, Dawson 3Pen: Grayson