The Thomastown man netted after just three minutes during a whirlwind start that yielded an unanswered 1-3 for Kilkenny and stood to them throughout.
Farrell’s second after 44 minutes was just as timely as it killed off Dublin in the midst of a spirited revival.
Richie Hogan, the only senior on the Kilkenny squad, wasn’t at his marauding best but still struck 0-5 to keep the county’s hopes of an All-Ireland treble alive.
With the minors and seniors already securing Leinster titles the U-21’s are now in a good position to push on too.
They’ll fancy their chances against the Ulster finalists in next month’s All-Ireland semi-final.
Dublin, who in contrast had several senior stars on board, battled bravely and had impressive performers in Peter Kelly who hit 1-3, Ronan Walsh and Simon Lambert.
But a generally bad night at the office for the Blues was compounded by the 58th minute injury that forced senior defender Oisín Gough to limp out of the action.
Anthony Daly will be hoping his corner-back is available for the All-Ireland senior quarter-finals in under 10 days time.
The tie was Kilkenny’s second serious test of the campaign after narrowly overcoming Offaly in the semi-finals.
They got a great start and racked up a sensational 1-3 without reply inside just three minutes.
Wing-forward John Mulhall shook off Paul Schutte inside the opening 30 seconds, laying down a marker for what lay ahead with a fine finish.
Mulhall scored Kilkenny’s second point before turning provider for James Nolan who played in Farrell for that third minute goal.
Michael Walsh’s Kilkenny were keen to prove a big point in front of a crowd of around 7,000 and threatened to dismiss Dublin by half-time.
But credit to the hosts who reeled off eight points before the break to pull themselves back into the game.
County seniors Liam Rushe and Kelly scored inspirational points for the Dubs but the scores always came that bit easier for Kilkenny.
Dublin got to within three points of the Cats twice but Kilkenny closed out the half as they’d started it with a scoring burst to win by seven.
Liam Ryan, Mulhall and Hogan were all on the mark to put Kilkenny into a healthy 1-12 to 0-8 half-time lead. Dublin restarted with back to back points from U-21 dual star Barry O’Rorke and Kelly.
But once again three points was the closest they would get to Kilkenny as the scores continued to come that bit easier for the visitors.
The game once again threatened to run away from Dublin when Kilkenny hit points from Farrell, Mark Kelly, James Nolan and Mulhall to lead 1-16 to 0-11.
But, as in the first-half, Dublin launched a mini revival to draw within three points again after 43 minutes. Peter Kelly’s goal was crucial to their revival as he followed up on Rushe’s initial shot to hit the net.
Farrell’s second goal just a minute later reopened Kilkenny’s six point lead and from there they never looked like losing.
There was a hint of fortune about the Cats’ second goal as Farrell seized on a poorly struck Hogan shot to hit the net from close range. Dublin outscored them 0-6 to 0-4 in the run in but Kilkenny were worthy winners.
KILKENNY: C McGrath; P Murphy, P Nolan, C Fogarty; M Walsh, D Langton, Lester Ryan; M Kelly (0-1), Liam Ryan (0-2); C Fennelly, M Bergin (0-4), J Mulhall (0-4); R Hogan (0-5; 4f), JJ Farrell (2-2), J Nolan (0-2).
Subs: K Hogan for Fennelly 56.
DUBLIN: F McGarry; G Kelly, M Quilty, O Gough; P Schutte, R O’Carroll, R Walsh; S Lambert (0-4; 2 65, 1f), C Clinton (0-3); P Kelly (1-3), D Treacy (0-3; 2f), P Garbutt (0-1; 1f); D O’Connor, L Rushe (0-2), B O’Rorke (0-2).
Subs: D Whelan for Garbutt 37, M May (0-1) for Schutte 40, J Sheanon for Lambert 49, D Kelly for O’Connor 50, D O Maoileidigh for Gough 58.
Referee: T Carroll (Offaly).