The 1-2 garnered in 11 minutes - equating to the margin at the end of Saturday's dour quarter-final replay in Thurles - seriously undermined Clare's challenge.
Powerful defensive play ultimately smothered their hopes.
Boy wonder Tommy Walsh, dismissed a week earlier, was inspirational while the recalled Michael Kavanagh was not far behind.
"We went at the game this time from the start. We let them dictate from the start last week," Kilkenny manager Brian Cody. "I never mind missing chances. I am always happy if we are creating chances, and we created a lot of chances this time."
Played in sweltering sun, the game was dominated for periods by the defensive approaches of both sides, with Cody matching Anthony Daly's deployment of an extra man in defence.
The net effect was to spoil it as a spectacle because so many attacks were suffocated by the extra man.
It wasn't pretty to watch. Daly, bitterly disappointed, but admitting to being "awful proud" of his players, pointed out that it was very different to the "feeling of shame" after the May 16 defeat by Waterford at the same venue. In retrospect he conceded that they had the best chance of winning the first day.
Kilkenny lined out with three changes in personnel, with Walsh operating at right half-back, while Clare made two alterations. One of them involved starting Brian Lohan at full-back, who only lasted eight minutes before being forced off with a hamstring injury. Brother Frank again took the role and once again excelled, helped by the fact that Shefflin's first touch left him down at stages. Daly described the absence of Tony Carmody (suffering from tonsillitis) as a major blow.
Shefflin, lining out at full-forward from the start, had the opening score from a third minute free before Eddie Brennan pointed from a ball he won in the square and which was diverted over the bar off a defender.
Minutes later he collected a Shefflin pass, rounded David Fitzgerald with ease for a simple goal. Given that he hardly touched the ball in the drawn game, this was a huge boost for the champions.
Very obviously fired up from the beginning, there was a determination in the Kilkenny play which enabled them to dictate the first 25 minutes, before they began to spurn chances. This coincided with Clare starting to drive forward more and more, with Alan Markham operating in and around the full-back line and sub Conor Plunkett doing well for a time at right half-back.
After Brennan got a second point in the 18th minute, Kilkenny were to remain scoreless for the rest of the half. Clearly, that would have concerned the management much more but for the fact that they were still winning plenty of ball up front, even though an obsession with goal-scoring was counter-productive. Vitally, their backs were extremely effective, with a highly motivated Walsh virtually unbeatable, against John Reddan and Jamesie O'Connor and Kavanagh thriving in the role of free man.
Noel Hickey and Peter Barry established early advantages in the central positions which they never really conceded for the 70 minutes and J.J. Delaney was again hugely influential.
Crucially, James Ryall had the beating of Niall Gilligan and, with Tony Griffin unable to penetrate, Clare really struggled for scores - in spite of the huge work-rate of Colin Lynch at midfield and some excellent work from their own defence, where Brian Quinn turned in a marvellous display.
It was 1-4 to 0-3 at the break.
The early second half was noteworthy for the fact that Kilkenny managed three points from placed balls, the third from a 65 struck by D.J. Carey who was to exert a growing influence in the half-forward line. Clare managed two in response, both from Gilligan frees (after substitute Barry Murphy had hit two wides immediately after the resumption), but they did no more than keep them in touch.
Nevertheless, Kilkenny were paying a price for their earlier misses by remaining vulnerable to a Clare recovery - except that a goal never materialised from several promising moves. Noel Hickey made a vital interception in the 43rd minute to deny Gilligan (now at full-forward after a spell on the wing) and with a bit of luck Gilligan might have scored 20 minutes later.
Then, James McGarry lost possession before the ball went wide off Gilligan. At this stage, only four points separated the sides and, when it mattered most, Kilkenny surged further ahead with two well-taken scores by Martin Comerford.
By now Shefflin was off the field, injured in suspicious circumstances, but Carey was giving great leadership when David Forde was very prominent at half-back before finishing in attack. Markham had started the half at centre-forward, but made no headway against the excellent Peter Barry and when Gilligan failed with an attempt at goal from a 25 yards free in the second last minute, nothing was going to alter the outcome.
Pat Horan did a good job of refereeing, imposing his authority without being over-assertive.
: Kilkenny - E. Brennan 1-2; D.J. Carey 0-3 (0-1 free, 0-1 seventy; H. Shefflin 0-3 frees; M. Comerford 0-2; J. Hoyne 0-1. Clare: N. Gilligan 0-3 frees; J. O'Connor 0-2; S. McMahon 0-2 frees; T. Griffin and D. Forde 0-1 each.
: J. McGarry; M. Kavanagh, N. Hickey, J. Ryall; T. Walsh, P. Barry, J.J. Delaney; D. Lyng, K. Coogan; M. Comerford (capt.), D.J. Carey, J. Hoyne; E. Brennan, H. Shefflin, J. Fitzpatrick. Subs: J. Maher for Shefflin (injured, 58th minute); S. Dowling for Coogan (65th).
: D. Fitzgerald; B. Quinn, B. Lohan, G. O'Grady; D. Hoey, S. McMahon, F. Lohan; C. Lynch, D. McMahon; J. Reddan, G. Quinn, A. Markham; N. Gilligan, T. Griffin, A. Quinn. Subs: C. Plunkett for F. Lohan (injured, 8th minute); J. O'Connor for A. Quinn (21st); D. Forde for Hoey (28th); B. Murphy for Reddan (second half); O. Baker for Markham (68th).
: P. Horan (Offaly).