Saracens will head into their Aviva Premiership Rugby semi-final against Gloucester on the crest of a wave after rounding off the regular season with an 11th consecutive victory.
Owen Farrell's second-half contribution of a try, conversion and penalty ultimately proved the difference after the two sides had been locked at 6-6. Farrell, the teenage fly-half who started the season on loan at Bedford, is now 80 minutes from guiding Saracens into the Aviva Premiership Rugby Final.
His performance was witnessed by England backs coach Brian Smith ahead of the forthcoming Churchill Cup, in which Farrell is sure to be involved. Chris Robshaw crossed for a consolation try but it was too little too late for Harlequins, who finish seventh in the Aviva Premiership Rugby table and miss out on automatic Heineken Cup qualification.
Conor O'Shea's men can still book their place in Europe's premier competition if they beat Stade Francais to win the Amlin Challenge Cup or if Northampton win the Heineken Cup.
Saracens were on course to finish the regular season top of the Aviva Premiership Rugby table until Leicester produced a dramatic comeback at Welford Road to beat London Irish. In the end, Saracens had to settle for second place and they will tackle Gloucester at Vicarage Road next Sunday for a place at Twickenham.
Saracens were beaten by the Tigers in last year's final but they have built up an impressive head of steam over the last three months. Many will consider them favourites. Even when unspectacular they are incredibly hard to beat as Harlequins, who came into the game on the back of a memorable victory over Munster last weekend, found to their cost.
The first half was a gritty affair, high on endeavour and ferocity if low on quality. After Clegg had missed an early shot at goal, Saracens wing David Strettle showed a sharp turn of pace and almost snatched a the ball away from covering Quins lock George Robson.
Goode nudged Saracens into a 6-0 lead with two penalties before tempers flared after Jacques Burger was felled by a dangerous-looking challenge, although referee Tim Wigglesworth took no action. Clegg landed his second attempt before Harlequins built a dangerous counter-attack through flanker Maurie Fa'asavalu, Robson and Ugo Monye. The Harlequins wing has been in impressive form of late but, with Stade Francais on the horizon, it will have been a concern to see him gingerly leaving the field early.
Harlequins built the pressure and earned a penalty under the Saracens posts, which Clegg struck with ease to draw the scores level at the interval. Saracens started the second half at a brisk pace with Strettle, competing with Monye for an England World Cup place, making an early break.
Schalk Brits twisted and turned for the line but was held up and, from the resulting scrum, Harlequins scrum-half Danny Care managed to force a mistake from Neil de Kock. But the Saracens pack then produced an almighty drive to push Harlequins off their own ball and De Kock fed Farrell who scored despite Monye's best efforts. Farrell converted and then landed a penalty to push Saracens 16-6 clear and into a winning position.
Harlequins – and Care in particular – began to grow increasingly frustrated with referee Wigglesworth as they tried to inject pace into the game late on. Burger was sin-binned late on for Saracens after a period of persistent Saracens offences and Robshaw galloped clear to score for Harlequins, but the Men In Black held on for the victory.