The young Dons had a lot of possession in the first half and then it was a case of trying to break down a well organised Kilmarnock side.
The opening goal came from a Connor Barron free kick. Connor, who has been called up to the Scotland U18 squad later this month, flighted over a ball into the box which came off an unfortunate defender who headed it pass his own goalkeeper.
No more than Aberdeen deserved at that stage.
The second goal came a minute into the second half.
Kieran Shanks did well and then played in Lewis Duncan who in turn played in Michael Dangana. Michael then put the ball across for Barron who stepped inside before finishing well. After a hat-trick of penalties against Celtic last time out, that is now the midfielder's fourth goal in two games.
After that Aberdeen looked quite safe and the home side never really created any clear cut chances that would have allowed them a way back into the game.
On a tight astro pitch the game then became quite scrappy but Barry Robson's side were able to comfortably see it out.
Coach Scott Anderson spoke to afc.co.uk after the game:
"Three points and a clean sheet is a good afternoon's work at our first away venue.
"It has been an encouraging start to the campaign. Barry has got them playing a decent style of football in terms of how they are passing the ball.
"It has been a positive start. Long may it continue."