The Dons went into the match hoping to record three consecutive wins for the first time this season but rarely troubled Cameron Bell in the Kilmarnock goal.
Goalmouth action was at a premium although Paul Heffernan should have netted a winner late on when he was thwarted by Aberdeen goalkeeper Jason Brown.
Andrew Considine returned from suspension to take his place in the heart of the home defence and was handed the captain's armband following the departure of Richard Foster to Bristol City.
Chris Clark also started for the Dons, who were without Peter Pawlett and Isaac Osbourne with both players having picked up hamstring injuries in the 4-0 win over Forfar in last weekend's William Hill Scottish Cup clash.
Kilmarnock, missing eight players through injury, handed a debut to new signing Ben Gordon, who has joined the Ayrshire club for his second loan spell from Chelsea.
Czech defender Zdenek Kroca was also drafted into the starting line-up, while there was a place on the bench for Michael Nelson who joined Killie after being released by Scunthorpe last week.
The Dons dropped to the bottom of the table when they lost 2-0 to the Ayrshire club at the start of December, however a run of 10 points in their previous five fixtures helped them move steadily up the table and away from the relegation zone.
Considine, who along with top scorer Scott Vernon signed a new deal to remain at Pittodrie this week, was called into action early on, heading away a Dean Shiels corner as Kilmarnock made a bright start.
The hosts had their first shot on goal after nine minutes but Bell comfortably saved Clark's low drive.
The visitors went much closer after 20 minutes when Garry Hay stung the palms of Brown in the Aberdeen goal with a powerful effort from 25 yards.
The Dons grew in confidence as the half wore on with a Fraser Fyvie shot bravely blocked by Hay with Kari Arnason heading over from the resulting corner.
Aberdeen had a scare at the other end when Brown fumbled a Shiels shot but the Welshman managed to gather the ball at the second attempt with Liam Kelly ready to pounce.
Aberdeen made a promising start to the second half with Mark Reynolds making a surging run past two Kilmarnock defenders before dragging a shot wide of the target.
Dons goalkeeper Brown looked nervous again as he fumbled a Danny Racchi shot when he should have made an easy save.
There were some angry scenes following a clash between Ryan Jack and Heffernan but referee Calum Murray managed to restore order without having to reach for his yellow card.
Racchi was unlucky not to get the opener after 66 minutes when his delicate chip just cleared the Aberdeen crossbar.
Killie made an attacking change after 72 minutes with French striker William Gros introduced at the expense of Hay.
But it was the Dons who were next to threaten when a far-post corner by Ryan Jack picked out Rory McArdle but the defender's header could only find the side-netting.
With time running out Aberdeen made a double change with Vernon and Mohamed Chalali replaced by Rory Fallon and Mitch Megginson.
But it was the visitors who should have won it at the death when Heffernan went through one-on-one with Brown but the Irishman shot straight at the goalkeeper.
Kilmarnock substitute Gros, who did not appear to be suffering from an injury, was withdrawn with four minutes remaining for Matthew Kennedy as the game came to a conclusion.