Referee Stephen Finnie waved away two strong penalty appeals from the home team in injury time which denied them the opportunity for a valuable equaliser.
Both teams had to re-shuffle their packs after losing their attacking focal points in the transfer window with Killie losing Steven Naismith and Craig Brewster leaving Pittodrie for the Inverness hot-seat which led to a disjointed first half with few clear chances.
The best chance of the half came in the 16th minute when Willie Gibson floated a cross to the far post for Ryan Jarvis, but the on-loan striker couldn't get good purchase in his effort when he should have scored.
Aberdeen showed more urgency after the break and worked two early openings for long-range shots which Alan Combe handled well.
Their new-found determination was rewarded after 52 minutes when the Dons took the lead.
Derek Young made the initial incursion, bursting past the defence to reach Barry Nicholson's through ball.
He collected the ball at an acute angle, but still managed to fire in a good shot which struck Combe's body and spun agonisingly wide of the post.
The goal was merely delayed as the home side failed to clear the resultant corner and were punished by Lee Miller, who flicked the ball over his shoulder and high into the net.
Killie pressed forward looking for an equaliser, but were denied by a resolute defence.
Gary Wales made a chance for himself in the 66th minute when he cut inside his marker, but Derek Soutar was equal to his shot.
Wales' afternoon ended in misery soon after when he was stretchered off with a nasty leg injury.
Steve Lovell cold have put the result beyond doubt in the 71st minute when he picked off a loose Simon Ford pass, but his touch deserted him and could only chip the ball to Combe.
Killie swept back up field and Allan Johnston fired in a thunderbolt which Richard Foster did well to deflect over.
Aberdeen were holding on in the dying minutes when Karim Touzani appeared to handle the ball on his own six-yard line and the referee waved play on, just as he did a minute later when Colin Nish was flattened by two defenders and Kilmarnock could not find the goal they deserved.