It seems that drama and Kilmarnock are somehow never far apart.

Kenny Shiels, the visiting manager, started his SFA ban sitting in the stand and relaying messages to Jimmy Nicholl, his assistant, directing Kilmarnock through a physical battle from which they ultimately emerged victorious.

Jamie Langfield, the Aberdeen goalkeeper, was sent off after he halted Borja Perez's 50-yard run into the area, giving the visitors a penalty kick which Liam Kelly ferociously converted.

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Kilmarnock's second goal, just before full time and again from Kelly, brought relief from the home side's pummelling of their opponents for long spells in the second half.

Shiels did not appear in the media room after the game, and Craig Brown, the Aberdeen manager, did not wish to comment on the penalty incident, perhaps mindful of his counterpart's spat with the SFA for his views about referees' decisions.

"If I had a gripe about the ordering-off," Brown said, "I wouldn't be voicing it. The first goal was a defining moment, but we dominated the game in the second half. It's a major concern that Perez managed to run through our midfield and our back three and get as close to the goal as he did. If he had put it into the back of the net I would have been questioning my team."

Shiels' vantage point afforded him a better view than Brown of proceedings and, early pressure from home team notwithstanding, it allowed him to attempt to work out a response to what seemed a curious Aberdeen formation.

Apart from a fourth-minute chance as Perez found space in the area from which to shoot a few inches past Langfield's left-hand post, Aberdeen had the majority of first-half possession, though their shoot-on-sight instructions did little to worry Cammy Bell, the Kilmarnock goalkeeper.

The visitors' patience contrasted with the more hurried approach of Aberdeen, keen to grab the opening goal so as not, in Brown's words, to have to again play "fight-back football".

However, with 45 minutes played Perez burst forward from inside his own half, catching the home defence off guard and almost inviting Langfield to fell him with an attempted save as he pushed the ball past the goalkeeper.

Rory Fallon, whose huffing and puffing had produced nothing, was immediately substituted for back-up keeper Jason Brown, whose first act was to pick out Kelly's penalty from his net.

Thus the second half began with Aberdeen instructed to do what they had sorely hoped to avoid and – a powerful header wide by Paul Heffernan from six yards out aside – they laid siege to their visitors.

The commitment from Aberdeen was palpable. Josh Magennis's 35-yard strike rattled Bell's crossbar and Niall McGinn, too, came close, with a 20-yard free-kick, the Kilmarnock goalkeeper having to be at his best to keep out the ball.

But for all their effort, energy and enthusiasm, it was Kilmarnock who again found the net. As the Aberdeen defence froze, Rory McKenzie's return ball found Kelly and he struck from the edge of the area, leaving Aberdeen still seeking their third home win of the season.

"The manager is always talking about the offensive side of the game, which is right," said Nicholl, "but recently we've been conceding goals. While the things we asked them to do probably sounded negative to the players, we just wanted a decent performance and to get something from the game. Aberdeen came at us and posed us problems in the second half, and we were grateful to see the second goal go in."