Quins dropped out of top flight for the first time in 18 years of competitive rugby, but would have escaped with victory had fly-half Jeremy Staunton landed a kickable 80th-minute penalty.
Staunton had scored the first of Harlequins' three tries just five minutes into the game, and kicked seven points, but the fly-half nudged his final kick wide with the whole season resting on it.
Quins boss Mark Evans said: "That was the most expensive kick in British rugby. They don't come any bigger than that at club level. Jeremy struck it really well, it just drifted wide of the left post. He's in bits but we'll pull him back together."
He added: "These things are decided on such small margins. There is such little difference between sixth and 12th. I don't think you can put your finger on any one thing we did wrong.
"We had a very poor start those first eight games when we lost put us in a difficult position. But there was never a stage when I thought we were doomed to go down."
Evans wants a speedy resolution to negotiations over the future of his star players as the club prepare for life in English rugby's second tier.
Some of the squad's bigger names such as Will Greenwood, Andre Vos, George Harder, Ugo Monye and Tony Diprose will be plundered by Quins' Premiership rivals and Evans wants them released as soon as possible.
He said: "We'll act quickly and get our contingency plans in place. We've already had a broad-brush look at what's going to happen with the senior players, now we need to sit down with them on Tuesday."
Irish aces Gavin Duffy, Simon Keogh and Staunton may also come up for grabs, and may be wooed back to the provincial system here.
For all Evans' hostility towards relegation, he could have few complaints following a dismal season in which all six of Quins' victories occurred during international weekends when their opponents were robbed of their best players.