Saracens, who will meet Toulon in the Heineken Cup decider next week, outscored their opponents three tries to two despite playing with 13 men for part of the first half after centre Marcelo Bosch and prop Matt Stevens were sent to the sin-bin.
They will meet Northampton in the Twickenham final in a fortnight after the Saints fought back from a 17-6 halftime deficit to beat holders Leicester 21-20 in the other semi on Friday.
After Saracens' Owen Farrell and Nick Evans of Harlequins traded early penalties, Saracens had both Bosch and Stevens sent off within five minutes of each other for a tip-tackle and deliberate knock-on respectively.
Harlequins took advantage of their numerical superiority when Ugo Monye touched down on 32 minutes.
Scottish flanker Kelly Brown hit back immediately for Saracens before England fullback Mike Brown, who later hobbled off injured, grabbed a further five-pointer on the stroke of halftime, with Evans' conversion handing Harlequins a 17-11 lead at the break.
Brad Barritt scored under the posts after 52 minutes for Saracens and 10 minutes later Chris Ashton, the leading try-scorer in the Heineken Cup this season, notched their third try.
The conversion and a further penalty by Farrell, his fourth, eased the 2010-11 champions to a 14-point winning margin and into their first Premiership final since their 2011 triumph.
(Reporting by Josh Reich; editing by Martyn Herman)
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