The centre-back made a decisive run and leap to meet Niall McGinn's 82nd-minute corner and head home from six yards to move the Dons above his former club, Motherwell, whose game against Inverness was postponed on Saturday.
The Dons dominated after half-time, although both goalkeepers made two good saves in the second half, and they were thankful for a dubious decision that robbed Kris Boyd of a goal during a first half that Kilmarnock largely controlled.
However the hosts paid for missing several good chances and a second late winner in five days, to follow Peter Pawlett's strike against Dundee United, earned Aberdeen their eighth win in nine games.
A first start for 17-year-old forward Robbie Muirhead meant there were seven homegrown players in the Killie line-up, including Boyd and Craig Samson.
Midfielder Craig Slater was the pick of the bunch as the Ayrshire side pushed forward for most of the first half, but Aberdeen had the first chance inside a minute when Pawlett released McGinn, who shot wide of the near post.
Killie should have been ahead in the 12th minute but for referee Craig Charleston's intervention.
Boyd appeared to brush Russell Anderson off fairly with a shoulder charge as the pair chased Jeroen Tesselaar's long ball but Charleston blew for a foul as the striker lobbed Jamie Langfield.
Both teams came close in the next four minutes. Ryan Jack headed Barry Robson's cross off the underside of the bar and then Boyd robbed Willo Flood and sprinted for goal, but Langfield came out quickly to block.
Killie had another good chance when Michael Hector, playing his last game before returning to Reading, made a hash of clearing Sean Clohessy's cross, but Chris Johnston skied his shot from 10 yards.
Another defensive lapse from the Dons gave Rory McKenzie a sniff of goal as he burst on to a short passback from left-back Jonny Hayes but Reynolds forced him wide and he could not test Langfield with his shot.
Killie continued to press and Johnston's effort spun off Anderson and landed on the roof of the net.
But Charleston upset the away fans when he penalised Pawlett for handball after the midfielder was chopped down by Manuel Pascali as he burst through on goal.
Samson saved from Hector and Jack either side of the break as Aberdeen moved the game into the Killie half.
But Kilmarnock were defending well and Langfield saved well from two Sammy Clingan free-kicks.
Aberdeen created a good chance as the game entered the final 15 minutes, although Pawlett appeared to push Pascali to gain an advantage. Charleston this time waved play on and Pawlett cut the ball back for McGinn 12 yards out but Samson dived low to his left to brilliantly stop the shot.
Aberdeen had another good chance when McGinn won the ball off McKenzie and drove forward before playing in Pawlett, but Samson stood up well to push over his powerful strike.
But the goal came from the resulting corner and Aberdeen held on after substitute Nicky Low was shown a straight red card in injury-time for lunging in on Clohessy after over-running the ball.