Aberdeen secured victory courtesy of a Lee Miller header in a hard-fought encounter at Rugby Park.
Goalscoring opportunities were at a premium as both sides missed recently-departed strikers.
Kilmarnock struggled without Steven Naismith after his £2m move to Rangers, while Aberdeen were without Craig Brewster, who left to manage Inverness.
Miller scored the only goal of the game after 54 minutes when he headed home from Michael Hart's flick-on.
Kilmarnock manager Jim Jefferies was forced into four changes following Naismith's last-minute move to Rangers and injuries to Danny Invincible, Ryan O'Leary and Garry Hay.
Simon Ford, Willie Gibson, Gary Wales and David Lilley came in as the Ayrshire side looked to continue their promising start to the season.
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Aberdeen boss Jimmy Calderwood, who has been linked with the vacant manager's post at Leicester, brought in Lee Miller and Steve Lovell up front after Craig Brewster returned to take charge of Inverness.
Calderwood handed Derek Young his first start since returning to the club and restored Richard Foster to the line-up.
Dons skipper Scott Severin and Zander Diamond were ruled out with Achilles injuries and Darren Mackie was on the bench.
Rhian Dodds had the first effort on goal after half an hour when his shot from the edge of the area scraped Soutar's crossbar and flew over.
The home fans claimed for a penalty when McNamara tangled with Nish after Allan Johnston's deep cross, but the referee waved away the appeals.
Lovell spurned a great chance just before half-time when he headed wide from 10 yards after a great cross from McNamara.
The visitors looked more threatening in the second half and took the lead in 54 minutes.
Jamie Smith's corner was headed on by Michael Hart and Miller made no mistake from 12 yards.
Kilmarnock pressed for an equaliser but clearly missed the creativity and goalscoring touch of Naismith.
Kilmarnock: Combe, Murray, Wright, Lilley, Ford, Johnston, Wales (Koudou 88), Dodds, Gibson, Jarvis (Fernandez 61), Nish. Subs Not Used: Harpur, Locke, Hamill, Clancy, Flannigan.
Booked: Wright.
Aberdeen: Soutar, Hart, Foster, McNamara, Considine, Clark, Nicholson, Jamie Smith, Young (Mackie 71), Miller, Lovell (Touzani 90). Subs Not Used: Langfield, Maguire, Jonathan Smith, Aluko, McVitie.
Goals: Miller 54.
Att: 5,814
Ref: S Finnie
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