A diving header from Paul Heffernan and a cool finish from Dean Shiels put Kilmarnock two ahead before Andrew Considine pulled a goal back after a mistake by Cameron Bell with 37 minutes gone.
The Dons equalised nine minutes after the restart when Youl Mawene headed home Kari Arnasoon's long throw into the box and looked the more likely to go on and take all three points but were unable to find a winner.
New Zealand international Rory Fallon made his Aberdeen debut while goalkeeper Jason Brown, who wore a black armband in tribute to the four men who died in the Swansea Valley mine tragedy, deputised for the unavailable David Gonzalez with Jamie Langfield on the bench for the first time since suffering a brain seizure during the summer.
Algerian striker Mohamed Chalali and youngster Ryan Jack also started for the Dons with Rory McArdle, Scott Vernon and Chris Clark all dropping to the bench.
Kilmarnock made two changes from the side that defeated Dunfermline 3-2 last weekend with Garry Hay and Slovenian Leon Panikvar preferred to Rory McKeown and Alex Pursehouse.
The Dons made a positive start to the match with skipper Richard Foster finding Fraser Fyvie in the box but the midfielder's acrobatic effort was bravely blocked by Panikvar after eight minutes.
Fyvie turned provider for the home side's next opportunity but debutant Fallon's header was comfortably held by Bell.
However it was the visitors who broke the deadlock after 15 minutes when Dean Shiels crossed for Heffernan who netted his fifth of the season with a superb diving header.
Kilmarnock doubled their advantage after 28 minutes when Hay surged at the home defence before releasing Shiels who slotted the ball past Brown.
The Dons were appealing for a penalty when Fallon fell under pressure from Gary Harkins but the former Plymouth striker was shown a yellow card for simulation.
But they pulled a goal back after 37 minutes when Bell flapped at Arnason's looping cross and Considine showed great composure to steer the ball into the unguarded net.
Aberdeen made a switch at the break with winger Peter Pawlett introduced at the expense of the ineffective Chalali.
The change gave the hosts fresh impetus and they restored parity after 54 minutes when Kilmarnock failed to deal with Arnason's long throw into the box and Mawene nodded the ball home.
The Dons went painfully close to finding a third when Milsom's free kick was headed on to the crossbar by Fallon after 62 minutes.
Aberdeen were enjoying a large amount of possession but Killie gave them a reminder that they were still in the game with Brown called upon to make a smart save to keep out Liam Kelly's rasping drive.
With less than 10 minutes remaining Chris Clark, a second-half substitute for Ryan Jack, flashed a shot wide of the target as the Reds continued their search for a winner.
Kilmarnock substitute Mohamadou Sissoko headed just over the bar in injury time as both sides had to settle for a share of the spoils.