It took just a few minutes for The Dons to create their first opening when a cross from the left found Logan at the back post, he brought the ball down and forced a smart stop from MacDonald at the near post. From the corner McLean flicked the ball towards goal but it was cleared by Boyd on that same near post.
Moments later there was another half chance for the hosts as MacDonald punched a corner clear to the edge of the box. Mackay-Steven had space to shoot but couldn't get the shot beyond the crowded six yard box and in the end the deflection fell kindly for the keeper.
Jordan Jones had found the net twice against The Dons already this season and after a quiet start on this occasion he popped up in the 16th minute to get a ball across the face of the goal, fortunately Logan was there to cut out the danger.
Up the other end McGinn was causing plenty of problems for Killie and almost found the opener when he picked the ball up on the edge of the box and found space to hit a powerful shot towards goal with no back lift, MacDonald did well to turn it over giving Aberdeen their 5th corner in just 20 minutes.
After a flurry of activity in the Kilmarnock half it was the visitors who broke up the other end and had a couple of half chances. In the 29th minute they took that threat one step further with Jones cutting inside, evading Ball and O'Connor before firing a shot towards goal. The shot hit off Kris Boyd and deflected into the back of the net giving Rogers no chance. It was a poor goal to concede as The Dons had chances to clear in the build-up.
Straight from the kick-off Aberdeen lost possession and Jones was on the march again, this time he cut inside and clipped the ball towards the far post and Rogers did well to push clear. It was an unsettling period for everyone inside Pittodrie as Kilmarnock started to take the game to the hosts.
Until the 40th minute there was no real pattern to the play as both teams battled for supremacy in the middle of the park, struggling to string many passes together. The Dons created another half chance when Mackay-Steven found half a yard out wide and clipped the ball in towards Rooney, in the end it was McGinn who connected but didn't get enough power on the shot to trouble the keeper.
In the 43rd minute Dicker picked up the first booking of the match for a foul on McLean. From the free-kick McKenna nodded the ball back across goal and Considine couldn't direct his header on target. At the break it was the visitors who led by one goal. They had executed their game plan well but you had to feel at this point that Aberdeen would be much improved in the second half.
There were no changes for The Dons at half-time but they did come out with a renewed focus and were rewarded just three minutes into the half when McKenna powered a header towards goal from a corner. The keeper looked to have stopped the ball but a combination of a bit of backspin and the attention of Adam Rooney ultimately ensured that The Dons drew level. The Aberdeen number 9 finding himself in the right place at the right time once again.
If the equaliser wasn't particularly pleasing on the eye the young centre half certainly made up for it two minutes later when he unleashed an unstoppable strike from at least 30 yards into the top corner of the net. MacDonald was left with no chance as Pittodrie erupted with players and management all rushing towards Scott as he celebrated the goal. It was one of the moments of the season so far and turned the match on its head.
Just after the hour mark McGinn found space on the left and floated the ball towards the back post and unfortunately for The Dons Logan just couldn't connect. After 63 minutes Dominic Ball was replaced by Arnason in a change which saw O'Connor move into midfield.
Out of nothing Killie had a free-kick 25 yards from goal which Boyd immediately took charge of. He hit a powerful strike towards goal through the gap in the wall which had been created by a striped shirt. Rogers stopped the initial strike and did enough to narrow the angle for Mulumbu who was first on the rebound.
It was a reminder that the visitors were still in the game but in the 72nd minute McGinn, who had performed well throughout, opened up a two goal advantage for The Dons. The winger won the ball in the Kilmarnock half and went all the way on his own before rifling the ball past MacDonald from 20 yards, it was an excellent goal.
Five minutes later McGinn almost picked out the opposite corner with another good strike but the ball fell just the wrong side of the post. Up the other end Considine was caught in possession which gave Brophy an opportunity to get to the by-line, his cutback found O'Donnell who looked certain to score but Rogers produced a fantastic save to knock the ball over the bar.
With just over five minutes of normal time remaining Chidi Nwakali made his debut for The Dons replacing Niall McGinn who had an excellent afternoon. Moments later the final change was made when Mackay-Steven was replaced by Scott Wright.
With just a couple of minutes remaining Nwakali picked up a yellow card for a foul on O'Donnell, it looked a bit harsh. As the clock turned to the 90th minute McLean had an opportunity to add a fourth when Nwakali played him through but the strike was pushed clear by MacDonald.
In the end the two goal lead would remain in place to send the red army home happy ahead of the midweek trip to Dingwall.