It was a heartbreaking defeat for Newcastle, who suffered more injury woes. Wingers Michael Stephenson and Tom May joined England's World Cup star Jonny Wilkinson on the sidelines.
May left the field after 60 minutes with a neck injury, while Stephenson has a suspected fractured elbow after crashing into the dug-out shortly after scoring a try that levelled the scores at 22-all.
The winning points, a try by prop Ceri Jones, came deep into injury time as the Falcons failed to protect a lead they had secured just minutes earlier.
Newcastle, who dominated the early exchanges without much reward, could have snatched victory in the end. They held a 25-22 lead, following a David Walder injury-time drop-goal. But Quins launched a final rush and prop Jones crashed over for the winning score.
In those early exchanges Quins were made to defend and that they certainly did very well, especially in the midfield where they often turned over ball.
While Quins had fewer chances, they took every chance that came their way. With their top flight back three of Gavin Duffy, George Harder and Will Greenwood together for the first time in many weeks they clearly had an edge out wide.
Ironically it was Newcastle who scored first, when David Walder kicked a penalty after two minutes, when a Quins player held on to the ball.
After nine minutes Quins showed just how dangerous they could be when Ugo Monye scored the first try. Newcastle had dominated, but the first chance Quins got on the attack they scored. It was totally against the run of play. Andy Dunne failed with the conversion attempt, but his team was in the lead.
David Walder missed with a penalty attempt for Newcastle in the 16th minute, before Quins scored again.
In the 20th minute Gavin Duffy score a try after a lapse in the Newcastle defence. They had again dominated play, but Quins took the chance when it came their way. Andy Dunne added the conversion for a 12-3 lead.
Newcastle's woes were illustrated in the 27th minute when they had a line-out just five metres out, but the throw went astray and then Quins got a penalty in the ensuing melee to bring some much needed relief.
Finally in 30th minute Newcastle got some reward for their efforts when Jamie Noon went over for their first try. David Walder added the conversion to narrow the gap to 12-10.
But Andy Dunne stretched the lead to 15-10, which was also the half-time score, when he slotted a penalty.
That lead was stretched even further when Jim Evans went over for an early second half try and Dunne slotted the conversion to make it 22-10 after 44 minutes.
But Newcastle continued to press hard and in the 59th minute they scored a well deserved try when flanker Epeli Taione went over. Walder added the conversion to narrow the gap to just five points.
The Falcons then levelled the scores when fullback Joe Shaw sprinted over for a try from a quick tap penalty.
Walder missed the conversion, but put his team in the lead with a drop-goal in injury time.
From the restart Quins pushed hard and they got a scrum just metres out. They threw everything into the ensuing maul and Ceri Jones was pushed over in the midst of a heap of bodies. Adrian Jarvis added the conversion to seal the win.
For the Newcastle Falcons:Try: Noon, Taione, ShawCons: Walder 2Pen: Walder DG: Walder
For NEC Harlequins:Tries: Monye, Duffy, Evans, JonesCons: Dunne 2, JarvisPen: Dunne