The home side had mixed news from the treatment room as Alan Combe was ruled out with a knee injury and Gary Locke's cold kept him at home while Boyd shook off his knee knock enough to start the match.
Aberdeen welcomed Scottish international Scott Severin back to the fold after a lengthy absence with a groin strain.
The Dons employed a five-man midfield but their numerical advantage was negated by Killie's full-backs powering forward at every opportunity to join the attack.
In a cagey first half, it was Graeme Smith who was first to shine as he threw himself to his left to fingertip Scott Morrison's 30-yard free-kick round the post.
Killie started to impose themselves with Gary McDonald and Allan Johnston both shooting high from good positions.
The home side's tactics seemed to be working better, but defensive lapses gifted chances to the Dons.
Simon Ford was guilty of a couple of losses of concentration but neither Darren Mackie nor John Stewart could capitalise. At the other end, a Russell Anderson mistake almost let Boyd in, but the skipper recovered to deny the hit-man and was alert enough to scoop the ball away from the waiting Colin Nish.
Killie had the perfect opportunity to go ahead at the interval when Richie Byrne whipped the legs from under Gary McDonald inside the area, but Ryan Esson dived full length to save Boyd's penalty. Indeed, from the rebound the Dons broke upfield and Smith had to be at his best to block Severin's powerful shot.
Smith produced another great stop seven minutes into the second half when Michael Hart broke out of defence. His angled shot seemed bound for the corner until Smith touched the ball behind.
Aberdeen upped the pace of their game and didn't allow Killie to get back into the game. Severin thought he had found the breakthrough when his 20-yard shot took a wicked deflection off Ford, but the spin took the ball wide.
Visiting substitute Steven Craig hit a rasping drive from the corner of the box, but again Smith was equal to it and the keeper found a bit of good luck as the ball rebounded between two attackers and was cleared to safety.
Smith was keeping Killie on the game, but even he was helpless with ten minutes left.
Kevin McNaughton picked the ball up on halfway and ran at the home defence. He left Peter Leven in his wake and fired a superb curling drive from 25 yards wide of the keeper and into the far corner for a stunning strike.
Aberdeen almost made it two in injury-time, but again Smith produced a fantastic double save - however the visitors ran out deserved winners.