Darren Mackie had a goal chalked off for offside and Javan Vidal shot wide in a painfully dull first period of the Saturday's SPL tussle.
But the visitors had the better openings in the second half with Jamie Hamill being denied excellently by Jamie Langfield before Craig Bryson hammered the ball off the post.
There was a place on the Dons bench for winger Jamie Smith following his return from injury, and he later came on for the closing minutes, but Richard Foster again missed out after his bust-up with Jimmy Calderwood.
Striker David Fernandez returned from suspension for Kilmarnock who made three changes to the side that lost 3-1 to Rangers.
Mehdi Taouil and Tim Clancy also started for the visitors with Grant Murray, Frazer Wright and Gavin Skelton missing out.
The Dons, unbeaten at home in the league since they defeated Kilmarnock at the start of November, immediately took the game to their opponents in this encounter.
The lively Chris Maguire found Sone Aluko in space on the left who sent an inviting cross into the area that Bryson did well to clear for a fruitless corner.
Bryson was then involved at the other end when he was booked for diving after falling under pressure from goalkeeper Langfield in the Aberdeen penalty area after 13 minutes.
Vidal almost grabbed an opener for the Dons after 19 minutes. The full-back, on loan from Manchester City, linked up with Mackie before surging into the box but his effort went inches wide of Alan Combe's goal.
The Aberdeen support thought their side had taken the lead after 22 minutes when Mackie volleyed home from a Charlie Mulgrew cross but the striker was penalised for straying into an offside position.
Kilmarnock defender David Lilley found himself in space to head Hamill's free-kick goalwards after 31 minutes but Langfield made a comfortable save.
Lee Mair did well to clear a Hamill cross with Fernandez lurking as the away side started to create more going forward.
A weak shot from Kevin Kyle was comfortably gathered by Langfield before Aluko was booked for kicking the ball away.
Willie Gibson replaced Taouil at the break for Kilmarnock who began the second half with the greater energy. They had a penalty appeal turned down within three minutes of the restart when Manuel Pascali collided with Lee Miller in the box.
And the visitors were unfortunate not to take the lead after 51 minutes when Mair misjudged Gibson's inviting cross but Langfield came to the defender's rescue by denying Hamill with an excellent stop.
A speculative effort from Mackie after 55 minutes did not trouble Combe as the game began to liven up.
Pascali was booked for a high challenge on Miller after 62 minutes, with Maguire joining him in the referee's notebook for persistent fouling a couple of minutes later.
Aberdeen made their first change after 66 minutes with Stuart Duff replacing Maguire.
The Dons were looking the more likely to score and brought Smith on after 74 minutes.
However the home side were given a scare when Bryson latched onto a neat Fernandez pass and hammered the ball off Langfield's post.
At the other end Mark Kerr should have done better when he swivelled in the box but fired his left-footed volley wide of the target.
The Dons continued to press for a winner with Aluko guilty of missing the target on two occasions in the final 10 minutes before Scott Severin had a goalbound effort cleared off the line.
Danny Invincibile replaced fellow substitute Gibson after 88 minutes.
The young Kilmarnock midfielder showed his disappointment of being taken off by storming up the tunnel before throwing his jersey onto the floor.
Conor Sammon came on for Fernandez in stoppage-time as Killie settled for a hard-fought point.