The winger was the most threatening player in a nervy encounter and got his first goal since returning to the Dons from a loan spell at Blackpool when he shot past Alan Combe from a tight angle early in the second half.
Kilmarnock piled on the pressure late on but the Dons stood firm for all three points.
Jimmy Calderwood made one change from the side that earned a point against Hearts at Tynecastle last week with Charlie Mulgrew starting ahead of Lee Mair, who dropped to the bench.
For Kilmarnock, Gavin Skelton and Conor Sammon replaced the injured duo of Frazer Wright and Danny Invincibile who both hobbled off in the midweek Co-operative Insurance Cup defeat to Celtic.
Aberdeen lined up with an attack-minded formation, with wing-backs Jared Hodgkiss and Mulgrew encouraged to get forward at every opportunity. However, it was the visitors who started brightest.
Slack defending from Aberdeen gave Manuel Pascali an early opportunity but Jamie Langfield managed to gather the Italian's effort at the second attempt.
The frenetic early pace continued when Aluko picked up the ball inside his own half and went on a surging run before firing harmlessly over Combe's bar from 20 yards.
A clever ball from Zander Diamond found Aluko at the edge of the box, and he unleashed a fierce shot that Combe did brilliantly to tip over.
From the resulting corner, desperate defending from David Lilley prevented Diamond opening the scoring with his head.
James Fowler picked up the first booking after 17 minutes for tripping Darren Mackie.
Langfield had to be alert to push a dipping effort from David Fernandez over the bar after good work by Mehdi Taouil.
At the other end Mulgrew had his first attempt from a free-kick after 30 minutes but his ambitious effort from 35 yards sailed well over the crossbar.
The Kilmarnock defence then struggled to deal with a long throw into the box from Scott Severin but when the ball eventually fell to Aluko, the young midfielder could not find the target.
Lee Miller had a great chance to net his fourth goal of the season from a Hodgkiss corner after 34 minutes when he out-jumped Pascali but his header went inches over.
Langfield was furious with his defence moments later when Jamie Hamill was allowed time and space to cut inside and shoot just past the post.
Aluko was Aberdeen's most promising outlet throughout the half and he did well to meet Mulgrew's cross but his volley crept wide of Combe's upright.
Mark Kerr came on to bolster the Aberdeen central midfield for the start of the second half at the expense of Mulgrew.
Kilmarnock had the first chance of the second period when an intelligent ball from Fernandez found Craig Bryson who unsuccessfully tried to square for Sammon when he should have shot himself.
But it was Aberdeen who opened the scoring five minutes into the second half in breathtaking style.
Aluko went on another mazy run down the left and as all in Pittodrie waited for him to cross for the waiting Miller or Mackie, the winger unleashed a piercing shot past Combe from the tightest of angles.
Aluko could have got his second after 58 minutes when he met a Miller cross on the volley but Hamill blocked the shot bravely.
Hamill was again the hero as he blocked Andrew Considine's goal-bound header on the line from a Derek Young corner.
Grant Murray was booked after 60 minutes for a foul on Miller as Aberdeen dominated proceedings. Former Dons defender Lilley joined Murray in the referee's book for another foul on Miller soon after.
Jim Jefferies brought Donovan Simmonds on for Sammon as Kilmarnock tried to get back in the game.
Simmonds almost had an immediate impact when he made a yard for himself on the edge of the box but he could not keep his powerful shot down.
William Gibson came on for the tiring Fernandez with 12 minutes to go as the Rugby Park side upped their efforts to get an equaliser.
Aluko was again terrorising the Killie defence and he bewildered Lilley but his eventual shot did not trouble Combe.
Aberdeen were given a warning with less than 10 minutes left when substitute Gibson put a dangerous ball into the penalty area that was just too high for the onrushing Hamill.
The pressure continued on a nervy Aberdeen defence when Hamill crossed but Langfield gathered under pressure from Skelton.
Langfield was then helpless as Simmonds crashed an effort off the bar in an absorbing final period.
Kilmarnock brought on David Cox for Taouil while Aluko and Young were replaced by Stuart Duff and Chris Maguire as the game drew to a close.
Duff could have sealed the points for the Dons in injury-time but Combe saved well at full stretch. Cox and Diamond were booked in angry scenes after the full-time whistle.