The teenage fly-half, already being tipped for senior England honours after less than a season in the Premiership, proved his big-match temperament by landing four penalties in blustery conditions to secure a repeat of last year's final showdown.
Gloucester came close to snatching the win with a breakaway try from fly-half Nicky Robinson when Saracens were down to 14 men.
But Farrell, whose charged down drop-goal attempt led to Gloucester's try, stepped up to land the decisive kick three minutes from time.
Saracens will be bent on revenge when they return to Twickenham on May 28, having been beaten by a last-minute Dan Hipkiss try in the final 12 months ago.
Mark McCall's men booked their title shot by grinding out a 12th consecutive victory in a scrappy encounter but the scoreline was far closer than it should have been.
Saracens were in control for the majority of the game but missed five of their seven first-half kicks at goal, which could have put them out of Gloucester's reach.
Three different kickers each missed a penalty attempt and James Short had a try disallowed all inside the opening nine minutes of the game.
Richard Wigglesworth took the first shot at goal from halfway and pulled it wide before Alex Goode carved through the Gloucester midfield to send Short away.
The Saracens wing appeared to have dived over in the corner but television replays showed Freddie Burns's last-ditch cover tackle had just forced his foot into touch.
Referee Andrew Small brought play back for a Saracens penalty but Goode fluffed it embarrassingly, prompting cries of "eeyore" from the sizeable travelling Gloucester contingent.
Farrell was the third Saracens player to miss inside nine minutes, striking the post with another long-range effort before eventually kicking his team on to the board at the fourth time of asking.
Gloucester's possession had been limited but, as ever, they looked dangerous with the ball in hand.
James Simpson-Daniel's quick thinking sparked a promising first Cherry and Whites attack, which stumbled when Robinson spilled the ball.
Although advantage was being played it was a strong attacking platform wasted and, to make matters worse, Robinson then missed his first shot at goal.
But Saracens were in control, with Schalk Brits jinking his way deep into the Gloucester half where the Men In Black won a penalty at the breakdown.
Farrell made no mistake from in front of the posts but missed his second, and Saracens' fourth, penalty attempt of the afternoon earned by a strong scrum.
That prompted Farrell to go for touch with his next effort and Saracens drove their lineout forward dangerously, with Ernst Joubert darting for the posts.
Gloucester held him up and Scott Lawson pinched possession to relieve the pressure, though they survived again before the interval when Farrell hit the post for a second time.
The visitors finished the half strongly with a Robinson penalty but it could have been better still had the fly-half not butchered a golden chance.
Robinson's midfield break had Saracens stretched but his long pass intended for Charlie Sharples flew over the wing's head and into touch.
Farrell edged Saracens into a 9-3 lead almost straight from the kick-off. Both he and Robinson then missed further attempts as the wind continued to play havoc.
There was a great deal of huff and puff, plenty of heavy tackles but it was pedestrian. There was very little creativity on show, a situation that suited Saracens down to the ground.
Now and again, Gloucester threatened to open the game up. Robinson's break and offload set the Cherry and Whites in motion but the move was brought to a thundering halt by Hugh Vyvyan's tackle on Rory Lawson, which put the scrum-half out of the game.
Saracens were reduced to 14 men in the 63rd minute after captain Steve Borthwick was judged to have taken Alex Brown out in the air and sent to the sin-bin.
The controversial touch-judge call revved up Saracens, who suddenly injected some urgency into proceedings - before being stung.
Farrell's drop-goal attempt was charged down by Brown and Akapusi Qera before Gloucester broke away, with Burns and Simpson-Daniel sending Robinson away under the posts.
Robinson's conversion edged Gloucester into the lead but Saracens responded almost immediately, with Vyvyan winning a breakdown penalty and Farrell landing his fourth penalty to seal the victory.
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