On-loan goalkeeper Freddie Woodman, who had a spell at Rugby Park last season, was the Dons hero as he made saves from Eamonn Brophy, Greg Taylor and Greg Kiltie in the shoot-out which saw Derek McInnes’ men prevail.
The teams could not be separated before then, Kenny McLean equalising from the spot in the first half of extra-time after Stephen O’Donnell’s breakthrough for Killie.
It ended the Ayrshire side’s dreams of a first semi-final since they won the trophy back in 1997 and they have now lost to Aberdeen on all ten occasions the clubs have met in the Scottish Cup.
It was palpably evident just how pivotal a contest this was for both clubs in terms of shaping the perception of their respective seasons. It was tetchy and fraught, the tension seemingly getting the better of both sets of players as they eyed the prize on offer.
Kilmarnock, with Kris Boyd deployed as the lone central striker in a shift away from Steve Clarke’s regularly favoured 4-4-2 set-up, resorted to a direct approach in the first half which caused the visitors few problems.
There was one early sight of goal for Killie’s in-form top scorer when he turned away from Anthony O’Connor but his tame shot was gathered with ease by Freddie Woodman.
Without producing much in the way of cohesive or progressive play themselves, Aberdeen carried a slight edge in terms of carrying a threat in a largely forgettable first half.
Adam Rooney would have expected to do better than slash a shot wildly off target in the 15th minute when he was picked out on the edge of the six yard box by Ryan Christie’s knockdown from a Gary Mackay-Steven cross.
Tempers flared midway through the opening period when Rory McKenzie showed more enthusiasm than was necessary in trying to retrieve the ball from under the prone figure of Mackay-Steven. McKenzie’s rugby-style rucking attempts to gain possession incensed Aberdeen and there was a melee involving players from both sides before referee Steven McLean restored order and decided a booking was sufficient punishment for the Killie midfielder.
Youssouf Mulumbu was struggling to make his mark in a creative sense for the hosts and his frustration boiled over when he conceded a cheap and dangerous free-kick on the edge of his own penalty area with a needless foul on Graeme Shinnie. Aberdeen were unable to take advantage as Niall McGinn scooped the ball way over the top.
Kenny McLean came much closer to a breakthrough for the Dons when he drilled a low shot narrowly wide of Jamie MacDonald’s left hand post from around 25 yards, then Scott McKenna hooked an effort just over following a corner as McInnes’ side tried to build some momentum.
But the general standard of play remained defiantly grim and there was little sign of improvement after the break. Kilmarnock had an optimistic claim for a penalty correctly dismissed by the officials as O’Connor made a well-timed challenge on Boyd early in the second half.
Clear cut chances were at an absolute premium and Boyd was unable to manufacture one when he got on the end of a Gary Dicker free-kick and saw his attempt to loft the ball back across the six yard box cut out by Woodman.
Jordan Jones, so often the man capable of providing a creative spark for Killie, had been seldom seen until he burst into life with a run and shot which at least forced a save from Woodman.
It began a sustained spell on the front foot for Clarke’s team as they increased the tempo of their work and Woodman was genuinely extended for the first time when he leapt to his right to keep out a stinging drive from Stephen O’Donnell.
Aberdeen responded with Christie coming close when he crashed a half volley just wide from 20 yards but there was to be no escape from extra-time which had seemed an inevitability for so long.
Finally, the tie burst into life with Killie taking the lead six minutes into the added period. Countering from an Aberdeen corner, Jones launched the ball for Eamonn Brophy to chase and the substitute held off Shay Logan before sliding a pass into the path of O’Donnell who beat Woodman with a cool finish.
Having waited so long for an advantage, Kilmarnock surrendered it cheaply just seven minutes later. Kirk Broadfoot’s senseless challenge on Stevie May conceded a clear penalty kick which McLean dispatched expertly beyond MacDonald.
McLean and Chidi Nwakali both came agonisingly close to winning it for Aberdeen but instead the tie went the full distance into the shoot-out.
Kilmarnock: MacDonald, O’Donnell, Broadfoot, Findlay, Taylor; Power (Tshibola 106), Dicker; McKenzie (Brophy 70), Mulumbu (Kiltie 118), Jones; K.Boyd (Erwin 91). Subs not used: Fasan, S. Boyd, Simpson.
Aberdeen: Woodman, Logan, O’Connor, McKenna, Considine; Shinnie, McLean; Christie (Nwakali 88), McGinn, Mackay-Steven (May 65); Rooney (Stewart 76). Subs not used: Rodgers, Reynolds, Arnason, Ball.