Chris Maguire converted a penalty after he had been fouled in the box by Kilmarnock' Frazer Wright and Rory McArdle headed Aberdeen's fourth.
Josh Magennis's drive completed the scoring eight minutes from time.
Killie's defeat allowed Motherwell to move to within two points of the Ayrshire side while Aberdeen are now four points clear of 10th-place Hibernian.
Aberdeen survived an early scare when Kieran Agard raced on to Alexei Eremenko's pass and knocked the ball past goalkeeper Jamie Langfield only to be tripped by Zander Diamond.
Diamond escaped punishment and Eremenko's free-kick was well saved by Langfield.
And the home side were soon ahead as Ryan Jack's low cross was not dealt with by Wright and Vernon squeezed a shot past Cammy Bell from 15 yards.
Maguire dragged a volley wide as Craig Brown's side imposed themselves.
And Aluko made the Dons' superiority count when he pounced on a loose ball and drilled a shot beyond Bell.
Another volley from Maguire drifted wide before the break.
Kilmarnock manager Mixu Paatelainen made changes at the break with Manuel Pascali and Jamie Hamill coming on for Rui Miguel and Liam Kelly.
But though alterations gave Killie more attacking impetus they were unable to work Langfield and before too long they were further behind.
Maguire was felled in the box by Wright, who was booked, and the striker sent Bell the wrong way from the spot.
Aluko's cross was headed back for McArdle to nod home Aberdeen's fourth goal in the 70th minute.
And Magennis added his name to the scoresheet when he pounced on Garry Hay's error and fired past Bell.
Sandy's Match Pic's are HERE
