Lewis Ferguson was the second time for Aberdeen's hero in a week, as his 87th minute free kick resulted in Kilmarnock's ninth consecutive victory.
Kilmarnock, who won the first domestic victory against Dons since December 2011, led by Kris Boyd.
The hosts dominated most of the game, but replaced by Bruce Anderson in Niall McGinn's shot.
And seven days after the Rangers champion winner, Ferguson made a small free kick at Jamie MacDonald.
He was hard on the home side with chances of Aberdeen before and after, Boyd was wide and Chris Burke and Alan Power shot at the bar.
"Boyd has an impact, then Kilmarnock falter"
Since Boyd started his career since August, he felt very early that veteran striker played a major role.
Even when an hour later he arrived at the Rugby Park before the game, the 35-year-old smiled a few light beats on his weight. The chance to recover you will come later.
Regardless of whether Boyd carries too much wood for a debate that is likely to run, but what was clearly evident was how much physical presence made it more difficult to protect Dons.
Kilmarnock deserved the goal from the step that caused the penalty – a rare glimpse into the passage and the flow that he started to figure out who? Boyd.
Elegant spin Jordan Jones was transfigured on the left and Stephen O'Donnell was at the disposal of internationals in Northern Ireland. Joe Lewis was a good player, but Shay Logan's challenge to Chris Burke started off with the ball.
Cue Boyd's Revenge. The punishment was placed in the lower left corner before the distant end. The strike spent the best 30 seconds on the Aberdeen fans who had great gangsters.
Testing for Michael Devlin and Scott McKenna with Boyd continued in the second half as he saw the former Rangers men's header at a few feet wide. But the game almost switched to Boyd instead.
Anderson had previously acquired Aberdeen from the tight situations and got to a point at Rangers at the opening weekend of the season. And this time, the 20-year-old man had cleverly kicked his leg to divert McGinn's simple shot of a desperate MacDonald.
Needless to say, Aberdeen fans will hear Boyd hear their joy and be better for travel enthusiasts.
Ferguson, in a less exploitative, offensive role, had a free kick 20 yards away and made a nasty finish in the lower right corner.
And where did Fergie celebrate? Before those great fans.
"McInnes keeps the winning record" – an analysis
Over the past eight days, Aberdeen progressed to the finals of the league cup, Hamilton was conveniently beaten at home and was the first to defeat Kilmarnock this week.
It could be a lucky win as Kilmarnock looked at at least the opening hours, but football matches could be the most unexpected.
Anderson, not for the first time this season, Aberdeen dug out of the tight spot. His promise and possibilities are positive, Ferguson's growing influence.
Kilmarnock will be curious that he did not take away anything from this game, but he was not only against Aberdeen at Rugby Park – McInnes won every time he was Dons boss.
The hosts are still in the top six places, although somewhere Aberdeen is still trying to settle this season.