Kilmarnock secured the three points which all but guaranteed a top-six finish in the SPL.
The first half produced little excitement as both sides cancelled each other out.
The first clear chance of the match came in the second minute of the second half when Alan Mahood crossed perfectly for Andy McLaren, but the Killie striker's powerful header flew past the far post.
The home side wasted another chance two minutes later when Gary McSwegan appeared to impede team-mate Garry Hay as the midfielder attacked Jamie Fowler's deep cross.
The turning point of the match came in the 55th minute when Eric Delomeaux, arguably Aberdeen's best player, reacted angrily to McLaren's challenge and was shown the red card. McLaren was booked for his part in the incident.
Aberdeen withdrew striker Laurent D’Jaffo for defender Kevin Rutkiewicz two minutes later, but the visitors were undone in the 59th minute when Russell Anderson's sloppy clearance fell at Gary McSwegan's feet 22 yards from goal and he instinctively sent the ball past Peter Kjaer into the bottom corner.
Worse was to follow for the Dons just four minutes later when James Fowler cleverly beat the offside trap and selfishly laid the ball off to Peter Canero who calmly tapped the ball into the empty net to continue his fine goalscoring run.
Kilmarnock used the extra man advantage well and home keeper Colin Meldrum was never seriously tested by the shot-shy Aberdeen attack.